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1

Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases.  

PubMed

A significant number of chimeric 16S rDNA sequences of diverse origin were identified in the public databases by partial treeing analysis. This suggests that chimeric sequences, representing phylogenetically novel non-existent organisms, are routinely being overlooked in molecular phylogenetic surveys despite a general awareness of PCR-generated artefacts amongst researchers. PMID:12656186

Hugenholtz, Philip; Huber, Thomas

2003-01-01

2

“A Faustian bargain?” Public voices on forensic DNA technologies and the National DNA Database  

Microsoft Academic Search

This article draws on the idea of the “forensic imaginary” (Williams 2010) to explore UK public perspectives on the place, role and significance of forensic DNA technologies, both independent of and in relation to other genetic applications. Using correspondents’ replies to the Spring 2006 Mass Observation Directive “Genes, Genetics and Cloning,” the analysis focuses on continuities and tensions in their

Dana Wilson-Kovacs; David Wyatt; Christine Hauskeller

2012-01-01

3

Forensic DNA databases  

Microsoft Academic Search

Genetic databases have been created in several countries: the United Kingdom was the first European country to have, in 1995, a DNA database. Subsequently, the Netherlands and Austria (1997), Germany (1998), Finland and Norway (1999) and many others have introduced or are preparing databases.Different national legal systems have conditioned the DNA databases and so there is a great heterogeneity between

Francisco Corte-Real

2004-01-01

4

A well placed trust?: Public perceptions of the governance of DNA databases  

Microsoft Academic Search

Biobanks that are run on an opt-in basis depend on people having the motivation to give and to trust in those who control their samples. Yet in the UK trust in the healthcare system has been in decline and there have been a number of health-related scandals that have received widespread media and public attention. Given this background, and the

Mairi Levitt; Sue Weldon

2005-01-01

5

Discrepancies between forensic DNA databases  

Microsoft Academic Search

In this study we present a comprehensive statistical comparison between a number of reference databases used in Sweden and two databases of DNA profiles from casework. Our results show no substantial differences with respect to various measurements of overall discrepancies but reveal significant differences for individual alleles at several loci.

Ronny Hedell; Anders Nordgaard; Ricky Ansell

6

Public chemical compound databases.  

PubMed

The internet has rapidly become the first port of call for all information searches. The increasing array of chemistry-related resources that are now available provides chemists with a direct path to the information that was previously accessed via library services and was limited by commercial and costly resources. The diversity of the information that can be accessed online is expanding at a dramatic rate, and the support for publicly available resources offers significant opportunities in terms of the benefits to science and society. While the data online do not generally meet the quality standards of manually curated sources, there are efforts underway to gather scientists together and 'crowdsource' an improvement in the quality of the available data. This review discusses the types of public compound databases that are available online and provides a series of examples. Focus is also given to the benefits and disruptions associated with the increased availability of such data and the integration of technologies to data mine this information. PMID:18428094

Williams, Anthony J

2008-05-01

7

AIDS PUBLIC INFORMATION DATABASE  

EPA Science Inventory

The AIDS Public Information Data Set is computer software designed to run on a Microsoft Windows microcomputer, and contains information abstracted from acquired immunodeficiency syndrome (AIDS) cases reported in the United States. The data set is created by the Division of HIV/A...

8

Database Support for Research in Public Administration  

ERIC Educational Resources Information Center

This study examines the extent to which databases support student and faculty research in the area of public administration. A list of journals in public administration, public policy, political science, public budgeting and finance, and other related areas was compared to the journal content list of six business databases. These databases

Tucker, James Cory

2005-01-01

9

Towards Privacy Preserving of Forensic DNA Databases  

E-print Network

Protecting privacy of individuals is critical for forensic genetics. In a kinship/identity testing, related DNA profiles between user's query and the DNA database need to be extracted. However, unrelated profiles cannot be revealed to each other...

Liu, Sanmin

2012-02-14

10

Forensic DNA profiling and database.  

PubMed

The incredible power of DNA technology as an identification tool had brought a tremendous change in crimnal justice . DNA data base is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. This article discusses the essential steps in compilation of COmbined DNA Index System (CODIS) on validated polymerase chain amplified STRs and their use in crime detection. PMID:23386793

Panneerchelvam, S; Norazmi, M N

2003-07-01

11

Forensic DNA Profiling and Database  

PubMed Central

The incredible power of DNA technology as an identification tool had brought a tremendous change in crimnal justice . DNA data base is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. This article discusses the essential steps in compilation of COmbined DNA Index System (CODIS) on validated polymerase chain amplified STRs and their use in crime detection. PMID:23386793

Panneerchelvam, S.; Norazmi, M.N.

2003-01-01

12

EMPOP--a forensic mtDNA database.  

PubMed

Mitochondrial DNA databases stand as the basis for frequency estimations of mtDNA sequences that became relevant in a case. The establishment of mtDNA databases sounds trivial; however, it has been shown in the past that this undertaking is prone to error for several reasons, particularly human error. We have established a concept for mtDNA data generation, analysis, transfer and quality control that meets forensic standards. Due to the complexity of mtDNA population data tables it is often difficult if not impossible to detect errors, especially for the untrained eye. We developed software based on quasi-median network analysis that visualizes mtDNA data tables and thus signposts sequencing, interpretation and transcription errors. The mtDNA data (N=5173; release 1) are stored and made publicly available via the Internet in the form of the EDNAP mtDNA Population Database, short EMPOP. This website also facilitates quasi-median network analysis and provides results that can be used to check the quality of mtDNA sequence data. EMPOP has been launched on 16 October 2006 and is since then available at http://www.empop.org. PMID:19083735

Parson, Walther; Dür, Arne

2007-06-01

13

Publications of Australian LIS Academics in Databases  

ERIC Educational Resources Information Center

This paper examines aspects of journal articles published from 1967 to 2008, located in eight databases, and authored or co-authored by academics serving for at least two years in Australian LIS programs from 1959 to 2008. These aspects are: inclusion of publications in databases, publications in journals, authorship characteristics of…

Wilson, Concepcion S.; Boell, Sebastian K.; Kennan, Mary Anne; Willard, Patricia

2011-01-01

14

Comparing the growth and effectiveness of forensic DNA databases  

Microsoft Academic Search

Forensic DNA databases have altered the landscape of the criminal justice system and re-shaped the field of forensic science. Whilst there has been widespread commentary regarding the legal and socio-political basis of DNA databases, there remains a lack of meaningful empirical assessment of database performance and effectiveness. In this research DNA database growth and effectiveness has been assessed statistically from

Simon J. Walsh; John S. Buckleton; Olivier Ribaux; Claude Roux; Tony Raymond

2008-01-01

15

Public Opinion Poll Question Databases: An Evaluation  

ERIC Educational Resources Information Center

This paper evaluates five polling resource: iPOLL, Polling the Nations, Gallup Brain, Public Opinion Poll Question Database, and Polls and Surveys. Content was evaluated on disclosure standards from major polling organizations, scope on a model for public opinion polls, and presentation on a flow chart discussing search limitations and usability.

Woods, Stephen

2007-01-01

16

Experimental Construction of VeryExperimental Construction of Very Large Scale DNA DatabasesLarge Scale DNA Databases  

E-print Network

, known as Watson-Crick complements.Watson-Crick complements. Recombinant DNA Operations:Recombinant DNAExperimental Construction of VeryExperimental Construction of Very Large Scale DNA DatabasesLarge Scale DNA Databases with Associative Search Capabilitywith Associative Search Capability DNA7DNA7 John H

Reif, John H.

17

CONSULTATION RESPONSE The Forensic Use of DNA and the National DNA Database  

E-print Network

CONSULTATION RESPONSE The Forensic Use of DNA and the National DNA Database Wellcome Trust response on the important topic of the forensic use of DNA and the National DNA Database (NDNAD). Given the Trust Assembly; "Forensic DNA Databasing: A European perspective" - a biomedical ethics grant to Professor Robin

Rambaut, Andrew

18

Artificial recombination in forensic mtDNA population databases  

Microsoft Academic Search

Artificial recombination of two or more mitochondrial DNA fragments from different samples would constitute a serious cause of error in forensic DNA typing, and yet one can demonstrate that such events have happened in the preparation of several published mtDNA databases. Focussed database searches, phylogenetic analysis, and network representations can highlight mosaic patterns and thus pinpoint sample mix-up. Therefore, we

H.-J. Bandelt; A. Salas; S. Lutz-Bonengel

2004-01-01

19

A compendium of human mitochondrial DNA control region: development of an international standard forensic database.  

PubMed

A compendium of human mitochondrial DNA (mtDNA) control region types has been constructed. This updated compilation indexes over 10,000 population-specific mtDNA nucleotide sequences in a standardized format. The sequences represent mtDNA types from the Scientific Working Group on DNA Analysis Methods (SWGDAM) mtDNA database and from the public literature. The SWGDAM data are considered to be of higher quality than the public data, particularly for counting the number of times a particular haplotype has been observed. PMID:11387646

Miller, K W; Budowle, B

2001-06-01

20

24 CFR 81.72 - Public-use database and public information.  

...2014-04-01 false Public-use database and public information. 81.72 ...Information § 81.72 Public-use database and public information. (a) General...available for public use, a public-use database containing public data as defined...

2014-04-01

21

24 CFR 81.72 - Public-use database and public information.  

Code of Federal Regulations, 2010 CFR

...2010-04-01 false Public-use database and public information. 81.72 ...Information § 81.72 Public-use database and public information. (a) General...available for public use, a public-use database containing public data as defined...

2010-04-01

22

24 CFR 81.72 - Public-use database and public information.  

Code of Federal Regulations, 2013 CFR

...2013-04-01 false Public-use database and public information. 81.72 ...Information § 81.72 Public-use database and public information. (a) General...available for public use, a public-use database containing public data as defined...

2013-04-01

23

24 CFR 81.72 - Public-use database and public information.  

Code of Federal Regulations, 2011 CFR

...2011-04-01 false Public-use database and public information. 81.72 ...Information § 81.72 Public-use database and public information. (a) General...available for public use, a public-use database containing public data as defined...

2011-04-01

24

24 CFR 81.72 - Public-use database and public information.  

Code of Federal Regulations, 2012 CFR

...2012-04-01 false Public-use database and public information. 81.72 ...Information § 81.72 Public-use database and public information. (a) General...available for public use, a public-use database containing public data as defined...

2012-04-01

25

EMPOP—A forensic mtDNA database  

Microsoft Academic Search

Mitochondrial DNA databases stand as the basis for frequency estimations of mtDNA sequences that became relevant in a case. The establishment of mtDNA databases sounds trivial; however, it has been shown in the past that this undertaking is prone to error for several reasons, particularly human error. We have established a concept for mtDNA data generation, analysis, transfer and quality

Walther Parson; Arne Dür

2007-01-01

26

Information Access through Electronic Databases for Rural Public Libraries.  

ERIC Educational Resources Information Center

To compile a list of recommended electronic databases for rural libraries, public library patron questions received by the Arizona State Reference Center were searched on ten databases. The results indicated Books in Print, Magazine Database, ABI/INFORM, Public Affairs Information System (PAIS), and Government Printing Office (GPO) Publications

Canepi, Kitti

1997-01-01

27

The Availability of Faculty Publication Databases from Library Web Pages  

ERIC Educational Resources Information Center

Faculty publication databases or author bibliographies offer libraries an opportunity to provide services to users. Initially, these databases remained initiatives of special libraries in the health-sciences fields. Librarians used the publication information derived from these databases to compile lists for annual reports. However, the advent of…

Blummer, Barbara A.

2007-01-01

28

Short Tandem Repeat DNA Internet Database  

NSDL National Science Digital Library

This website contains comprehensive information relating to forensic DNA analysis. It has material from an introductory to an advanced level on forensic DNA technology. The material provides general information on DNA markers that are of interest to human identification. The site contains both introductory and in-depth discussions of short tandem repeats (STRs) and other DNA markers currently used by the forensic community. Powerpoint and PDF presentations on STR training material are available and can be readily downloaded.

2011-04-08

29

Forensic DNA databases: genetic testing as a societal choice  

Microsoft Academic Search

In this brief report, the authors argue that while a lot of concerns about forensic DNA databases have been raised using arguments from biomedical ethics, these databases are used in a complete different context from other biomedical tools. Because they are used in the struggle against crime, the decision to create or store a genetic profile cannot be left to

Annemie Patyn; Kris Dierickx

2010-01-01

30

Database Connects Public to University of Nebraska Research  

E-print Network

Database Connects Public to University of Nebraska Research By Steve Ress There's a wealth of water easier. An easily accessible and searchable database sponsored by the University of Nebraska Rachael Herpel, outreach and education specialist at the UNL Water Center. The database can be found

Nebraska-Lincoln, University of

31

Exploration of the Chemical Space of Public Genomic Databases  

EPA Science Inventory

The current project aims to chemically index the content of public genomic databases to make these data accessible in relation to other publicly available, chemically-indexed toxicological information. ...

32

Belgian dog mitochondrial DNA database for forensics  

Microsoft Academic Search

A Belgian population sample of 117 unrelated breed dogs and mongrels, was mitochondrial DNA profiled by sequencing the two hypervariable regions HV1 and HV2. The complete control region of each dog was amplified in a single PCR. The combination of eight sequencing reactions compiles the mtDNA profile, of which each position was covered at least twice. 48 haplotypes were identified,

Stijn Desmyter; Sylvie Comblez

2009-01-01

33

Cryptographic Approaches to Provacy in Forensic DNA Databases  

Microsoft Academic Search

Advances in DNA sequencing technology and human genetics are leading to the availabilityof inexpensive genetic tests, notably tests for individual predisposition to certain diseases. Whilesuch information is often valuable, its availability has raised serious concerns over the privacyof genetic information. These concerns are further heightened when genetic information isgathered into databases. We study access control for one class of such

Philip Bohannon; Markus Jakobsson; Sukamol Srikwan

2000-01-01

34

The Israel DNA database--the establishment of a rapid, semi-automated analysis system.  

PubMed

The Israel Police DNA database, also known as IPDIS (Israel Police DNA Index System), has been operating since February 2007. During that time more than 135,000 reference samples have been uploaded and more than 2000 hits reported. We have developed an effective semi-automated system that includes two automated punchers, three liquid handler robots and four genetic analyzers. An inhouse LIMS program enables full tracking of every sample through the entire process of registration, pre-PCR handling, analysis of profiles, uploading to the database, hit reports and ultimately storage. The LIMS is also responsible for the future tracking of samples and their profiles to be expunged from the database according to the Israeli DNA legislation. The database is administered by an in-house developed software program, where reference and evidentiary profiles are uploaded, stored, searched and matched. The DNA database has proven to be an effective investigative tool which has gained the confidence of the Israeli public and on which the Israel National Police force has grown to rely. PMID:21727053

Zamir, Ashira; Dell'Ariccia-Carmon, Aviva; Zaken, Neomi; Oz, Carla

2012-03-01

35

Enhancing thermal video using a public database of images  

NASA Astrophysics Data System (ADS)

We presented a system to display nightime imagery with natural colors using a public database of images. We initially combined two spectral bands of images, thermal and visible, to enhance night vision imagery, however the fused image gave an unnatural color appearance. Therefore, a color transfer based on look-up table (LUT) was used to replace the false color appearance with a colormap derived from a daytime reference image obtained from a public database using the GPS coordinates of the vehicle. Because of the computational demand in deriving the colormap from the reference image, we created an additional local database of colormaps. Reference images from the public database were compared to a compact local database to retrieve one of a limited number of colormaps that represented several driving environments. Each colormap in the local database was stored with an image from which it was derived. To retrieve a colormap, we compared the histogram of the fused image with histograms of images in the local database. The colormaps of the best match was then used for the fused image. Continuously selecting and applying colormaps using this approach offered a convenient way to color night vision imagery.

Qadir, Hemin; Kozaitis, S. P.; Ali, Ehsan

2014-05-01

36

Forensic DNA Sampling and the England and Wales National DNA Database: A Sceptical Approach  

Microsoft Academic Search

This paper explores possible implications of the rapid expansion of the England and Wales National DNA Database (NDNAD), and\\u000a the current DNA sampling of offenders and the retention of samples. A precis of the justifications enunciated for the NDNAD\\u000a is followed by a sceptic's rebuttal and wider analysis of the impact of the growth of forensic DNA testing. It is

Carole Mccartney

2004-01-01

37

Launching the Greek forensic DNA database. The legal framework and arising ethical issues  

Microsoft Academic Search

Since the creation of the first national DNA database in Europe in 1995, many European countries have legislated laws for initiating and regulating their own databases.The Greek government legislated a law in 2008, by which the National DNA Database of Greece was founded and regulated. According to this law, only DNA profiles from convicted criminals were recorded. Nevertheless, a year

Polychronis Voultsos; Samuel Njau; Nikolaos Tairis; Dimitrios Psaroulis; Leda Kovatsi

2011-01-01

38

Building a Faculty Publications Database: A Case Study  

ERIC Educational Resources Information Center

This case study shares the experience of building an in-house faculty publications database that was spearheaded by the Touro College and University System library in 2010. The project began with the intention of contributing to the college by collecting the research accomplishments of our faculty and staff, thereby also increasing library…

Tabaei, Sara; Schaffer, Yitzchak; McMurray, Gregory; Simon, Bashe

2013-01-01

39

DATABASE LIKELIHOOD RATIOS AND FAMILIAL DNA KLAAS SLOOTEN AND RONALD MEESTER  

E-print Network

DATABASE LIKELIHOOD RATIOS AND FAMILIAL DNA SEARCHING KLAAS SLOOTEN AND RONALD MEESTER Abstract. Familial Searching is the process of searching in a DNA database for relatives of a given individual ratio, which is in this context called a Kinship Index. Suppose that the database contains, for a given

Meester, Ronald

40

mtGenome reference population databases and the future of forensic mtDNA analysis  

Microsoft Academic Search

Mitochondrial DNA (mtDNA) testing in the forensic context requires appropriate, high quality population databases for estimating the rarity of questioned haplotypes. Currently, however, available forensic mtDNA reference databases only include information from the mtDNA control region. While this information is obviously strengthening the foundation upon which current mtDNA identification efforts are based, these data do not adequately prepare the field

Jodi A. Irwin; Walther Parson; Michael D. Coble; Rebecca S. Just

2011-01-01

41

Genetics and Forensics: Making the National DNA Database  

PubMed Central

This paper is based on a current study of the growing police use of the epistemic authority of molecular biology for the identification of criminal suspects in support of crime investigation. It discusses the development of DNA profiling and the establishment and development of the UK National DNA Database (NDNAD) as an instance of the ‘scientification of police work’ (Ericson and Shearing 1986) in which the police uses of science and technology have a recursive effect on their future development. The NDNAD, owned by the Association of Chief Police Officers of England and Wales, is the first of its kind in the world and currently contains the genetic profiles of more than 2 million people. The paper provides a framework for the examination of this socio-technical innovation, begins to tease out the dense and compact history of the database and accounts for the way in which changes and developments across disparate scientific, governmental and policing contexts, have all contributed to the range of uses to which it is put. PMID:16467921

Johnson, Paul; Williams, Robin; Martin, Paul

2005-01-01

42

SSAHA: a fast search method for large DNA databases.  

PubMed

We describe an algorithm, SSAHA (Sequence Search and Alignment by Hashing Algorithm), for performing fast searches on databases containing multiple gigabases of DNA. Sequences in the database are preprocessed by breaking them into consecutive k-tuples of k contiguous bases and then using a hash table to store the position of each occurrence of each k-tuple. Searching for a query sequence in the database is done by obtaining from the hash table the "hits" for each k-tuple in the query sequence and then performing a sort on the results. We discuss the effect of the tuple length k on the search speed, memory usage, and sensitivity of the algorithm and present the results of computational experiments which show that SSAHA can be three to four orders of magnitude faster than BLAST or FASTA, while requiring less memory than suffix tree methods. The SSAHA algorithm is used for high-throughput single nucleotide polymorphism (SNP) detection and very large scale sequence assembly. Also, it provides Web-based sequence search facilities for Ensembl projects. PMID:11591649

Ning, Z; Cox, A J; Mullikin, J C

2001-10-01

43

A publication database for optical long baseline interferometry  

E-print Network

Optical long baseline interferometry is a technique that has generated almost 850 refereed papers to date. The targets span a large variety of objects from planetary systems to extragalactic studies and all branches of stellar physics. We have created a database hosted by the JMMC and connected to the Optical Long Baseline Interferometry Newsletter (OLBIN) web site using MySQL and a collection of XML or PHP scripts in order to store and classify these publications. Each entry is defined by its ADS bibcode, includes basic ADS informations and metadata. The metadata are specified by tags sorted in categories: interferometric facilities, instrumentation, wavelength of operation, spectral resolution, type of measurement, target type, and paper category, for example. The whole OLBIN publication list has been processed and we present how the database is organized and can be accessed. We use this tool to generate statistical plots of interest for the community in optical long baseline interferometry.

Malbet, Fabien; Lawson, Peter; Taillifet, Esther; Lafrasse, Sylvain

2010-01-01

44

A publication database for optical long baseline interferometry  

NASA Astrophysics Data System (ADS)

Optical long baseline interferometry is a technique that has generated almost 850 refereed papers to date. The targets span a large variety of objects from planetary systems to extragalactic studies and all branches of stellar physics. We have created a database hosted by the JMMC and connected to the Optical Long Baseline Interferometry Newsletter (OLBIN) web site using MySQL and a collection of XML or PHP scripts in order to store and classify these publications. Each entry is defined by its ADS bibcode, includes basic ADS informations and metadata. The metadata are specified by tags sorted in categories: interferometric facilities, instrumentation, wavelength of operation, spectral resolution, type of measurement, target type, and paper category, for example. The whole OLBIN publication list has been processed and we present how the database is organized and can be accessed. We use this tool to generate statistical plots of interest for the community in optical long baseline interferometry.

Malbet, Fabien; Mella, Guillaume; Lawson, Peter; Taillifet, Esther; Lafrasse, Sylvain

2010-07-01

45

Seattle Public Library Web Sites and Databases: Municipal Codes Online  

NSDL National Science Digital Library

Drawing heavily on the Folio databases made available by the Municipal Code Corporation, as well as other sources, Jeannette Voiland of the Seattle Public Library has compiled a growing list of over 150 municipal codes in 37 states at this time. Depth of coverage varies by state, with especially good coverage for Florida, California, and Washington. As the site grows, it should become a major repository for US municipal code information.

1997-01-01

46

“It all happened so slowly” – On controlling function creep in forensic DNA databases  

Microsoft Academic Search

Forensic DNA databases are implemented worldwide and used increasingly. Part of this increasing usage is arguably a matter of function creep. Function creep refers to changes in, and especially additions to, the use of a technology. In this article we explore the notion of function creep as we discuss why and how it has taken place on forensic DNA databases.

Johanne Yttri Dahl; Ann Rudinow Sætnan

2009-01-01

47

Forensic DNA databases in England and the Netherlands: governance, structure and performance compared  

Microsoft Academic Search

How do liberal democracies govern forensic DNA databasing? That is the question being asked in this contribution by focusing on the rules for inclusion of samples\\/profiles in DNA databases in England and Wales and the Netherlands. The two different modes of governance shall be evaluated by taking into account models and ideas in each society regarding the two imperatives of

Victor Toom

2012-01-01

48

High-throughput STR analysis for DNA database using direct PCR.  

PubMed

Since the Korean criminal DNA database was launched in 2010, we have focused on establishing an automated DNA database profiling system that analyzes short tandem repeat loci in a high-throughput and cost-effective manner. We established a DNA database profiling system without DNA purification using a direct PCR buffer system. The quality of direct PCR procedures was compared with that of conventional PCR system under their respective optimized conditions. The results revealed not only perfect concordance but also an excellent PCR success rate, good electropherogram quality, and an optimal intra/inter-loci peak height ratio. In particular, the proportion of DNA extraction required due to direct PCR failure could be minimized to <3%. In conclusion, the newly developed direct PCR system can be adopted for automated DNA database profiling systems to replace or supplement conventional PCR system in a time- and cost-saving manner. PMID:23683293

Sim, Jeong Eun; Park, Su Jeong; Lee, Han Chul; Kim, Se-Yong; Kim, Jong Yeol; Lee, Seung Hwan

2013-07-01

49

An assessment of whether SNPs will replace STRs in national DNA databases Joint considerations of the  

E-print Network

of the DNA working group of the European Network of Forensic Science Institutes (ENFSI) and the Scientific Working Group on DNA Analysis Methods (SWGDAM) Sir: It is unlikely that SNPs will replace STRsAn assessment of whether SNPs will replace STRs in national DNA databases ­ Joint considerations

50

Evaluating DNA profile evidence when the suspect is identified through a database search  

Microsoft Academic Search

ABSTRACT: The paper is concerned with the strength of DNA evidence when a suspect is identified via a search through a database of the DNA profiles of known,individuals. Consideration of the appropriate likelihood ratio shows that in this setting the DNA evidence is (slightly) stronger than when,a suspect is identified by other means, subsequently profiled, and found to match. The

Dj Balding; P Donnelly

1996-01-01

51

DSSTOX WEBSITE LAUNCH: IMPROVING PUBLIC ACCESS TO DATABASES FOR BUILDING STRUCTURE-TOXICITY PREDICTION MODELS  

EPA Science Inventory

DSSTox Website Launch: Improving Public Access to Databases for Building Structure-Toxicity Prediction Models Ann M. Richard US Environmental Protection Agency, Research Triangle Park, NC, USA Distributed: Decentralized set of standardized, field-delimited databases,...

52

Forensic DNA databases in Western Balkan region: retrospectives, perspectives, and initiatives  

PubMed Central

The European Network of Forensic Science Institutes (ENFSI) recommended the establishment of forensic DNA databases and specific implementation and management legislations for all EU/ENFSI members. Therefore, forensic institutions from Bosnia and Herzegovina, Serbia, Montenegro, and Macedonia launched a wide set of activities to support these recommendations. To assess the current state, a regional expert team completed detailed screening and investigation of the existing forensic DNA data repositories and associated legislation in these countries. The scope also included relevant concurrent projects and a wide spectrum of different activities in relation to forensics DNA use. The state of forensic DNA analysis was also determined in the neighboring Slovenia and Croatia, which already have functional national DNA databases. There is a need for a ‘regional supplement’ to the current documentation and standards pertaining to forensic application of DNA databases, which should include regional-specific preliminary aims and recommendations. PMID:21674821

Marjanovic, Damir; Konjhodzic, Rijad; Butorac, Sara Sanela; Drobnic, Katja; Merkas, Sinisa; Lauc, Gordan; Primorac, Damir; An?elinovic, Simun; Milosavljevic, Mladen; Karan, Zeljko; Vidovic, Stojko; Stojkovic, Oliver; Panic, Bojana; Vucetic Dragovic, An?elka; Kovacevic, Sandra; Jakovski, Zlatko; Asplen, Chris; Primorac, Dragan

2011-01-01

53

Strengthening the united states’ database protection laws: Balancing public access and private control  

Microsoft Academic Search

This paper develops three arguments for increasing the strength of database protection under U.S. law. First, stronger protections\\u000a would encourage private investment in database development, and private databases have many potential benefits for science\\u000a and industry. Second, stronger protections would discourage extensive use of private licenses to protect databases and would\\u000a allow for greater public control over database laws and

David B. Resnik

2003-01-01

54

The EpiSLI Database: A Publicly Available Database on Speech and Language  

ERIC Educational Resources Information Center

Purpose: This article describes a database that was created in the process of conducting a large-scale epidemiologic study of specific language impairment (SLI). As such, this database will be referred to as the EpiSLI database. Children with SLI have unexpected and unexplained difficulties learning and using spoken language. Although there is no…

Tomblin, J. Bruce

2010-01-01

55

Likelihood Ratios for Evaluating DNA Evidence When the Suspect is Found Through a Database Search  

Microsoft Academic Search

SUMMARY. A crime has been committed, and a DNA profile of the perpetrator is obtained from the crime scene. A suspect with a matching profile is found. The problem of evaluating this DNA evidence in a forensic context, when the suspect is found through a database search, is analysed through a likelihood approach. The recommendations of the National Research Council

Anders Stockmarr

1999-01-01

56

Inspecting close maternal relatedness: Towards better mtDNA population samples in forensic databases  

Microsoft Academic Search

Reliable data are crucial for all research fields applying mitochondrial DNA (mtDNA) as a genetic marker. Quality control measures have been introduced to ensure the highest standards in sequence data generation, validation and a posteriori inspection. A phylogenetic alignment strategy has been widely accepted as a prerequisite for data comparability and database searches, for forensic applications, for reconstructions of human

Martin Bodner; Jodi A. Irwin; Michael D. Coble; Walther Parson

2011-01-01

57

The Problem Child: Forensic DNA Databases, Familial Search, and A Call for Reform  

Microsoft Academic Search

The FBI’s Combined DNA Index System (CODIS) and its component databases are expanding rapidly. Originally profiling only certain classes of convicted violent felons, CODIS now includes all federal arrestees, convicts, and foreign detainees, as well as convicts from every state and arrestees from many. This expansion is driven by the desire to solve more crimes with forensic DNA evidence, which

Michael Seringhaus

2010-01-01

58

A study of Spanish attitudes regarding the custody and use of forensic DNA databases  

Microsoft Academic Search

One of the issues that has resulted in much disagreement in many countries at different levels concerns the kind of institution that should be given the responsibility of exercising custody over biological samples and the DNA profiles obtained from these samples.In the field of forensic genetics, there is no doubt that the existence of DNA criminal databases benefits the control

Joaquín-Jose Gamero; José-Luis Romero; Juan-Luis Peralta; Francisco Corte-Real; Margarita Guillén; Maria-Joao Anjos

2008-01-01

59

Prisoners’ expectations of the national forensic DNA database: Surveillance and reconfiguration of individual rights  

Microsoft Academic Search

In this paper we aim to discuss how Portuguese prisoners know and what they feel about surveillance mechanisms related to the inclusion and deletion of the DNA profiles of convicted criminals in the national forensic database. Through a set of interviews with individuals currently imprisoned we focus on the ways this group perceives forensic DNA technologies. While the institutional and

Helena Machado; Filipe Santos; Susana Silva

2011-01-01

60

The relative flexibility of B-DNA and A-RNA duplexes: database analysis  

PubMed Central

An extensive analysis of structural databases is carried out to investigate the relative flexibility of B-DNA and A-RNA duplexes in crystal form. Our results show that the general anisotropic concept of flexibility is not very useful to compare the deformability of B-DNA and A-RNA duplexes, since the flexibility patterns of B-DNA and A-RNA are quite different. In other words, ‘flexibility’ is a dangerous word for describing macromolecules, unless it is clearly defined. A few soft essential movements explain most of the natural flexibility of A-RNA, whereas many are necessary for B-DNA. Essential movements occurring in naked B-DNAs are identical to those necessary to deform DNA in DNA–protein complexes, which suggest that evolution has designed DNA–protein complexes so that B-DNA is deformed according to its natural tendency. DNA is generally more flexible, but for some distortions A-RNA is easier to deform. Local stiffness constants obtained for naked B-DNAs and DNA complexes are very close, demonstrating that global distortions in DNA necessary for binding to proteins are the result of the addition of small concerted deformations at the base-pair level. Finally, it is worth noting that in general the picture of the relative deformability of A-RNA and DNA derived from database analysis agrees very well with that derived from state of the art molecular dynamics (MD) simulations. PMID:15562006

Pérez, Alberto; Noy, Agnes; Lankas, Filip; Luque, F. Javier; Orozco, Modesto

2004-01-01

61

KATANA: A web-based guide to public databases for Arabidopsis genomic information  

Microsoft Academic Search

Genomic information of Arabidopsis thaliana can be obtained from various public databases. Given that naming conventions often vary between databases and that the same genes can be annotated differently, we developed a web-based tool, KATANA (Kazusa Arabidopsis thaliana Annotation Abstract; http:\\/\\/www.kazusa.or.jp\\/katana\\/), to guide users searching for Arabidopsis genomic information to the relevant public databases from a single site. The tool

Kentaro Yano; Tomoko Dansako; Nozomu Sakurai; Hideyuki Suzuki; Daisuke Shibata

62

BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources  

PubMed Central

Background DNA barcoding provides a rapid, accurate, and standardized method for species-level identification using short DNA sequences. Such a standardized identification method is useful for mapping all the species on Earth, particularly when DNA sequencing technology is cheaply available. There are many nations in Asia with many biodiversity resources that need to be mapped and registered in databases. Results We have built a general DNA barcode data processing system, BioBarcode, with open source software - which is a general purpose database and server. It uses mySQL RDBMS 5.0, BLAST2, and Apache httpd server. An exemplary database of BioBarcode has around 11,300 specimen entries (including GenBank data) and registers the biological species to map their genetic relationships. The BioBarcode database contains a chromatogram viewer which improves the performance in DNA sequence analyses. Conclusion Asia has a very high degree of biodiversity and the BioBarcode database server system aims to provide an efficient bioinformatics protocol that can be freely used by Asian researchers and research organizations interested in DNA barcoding. The BioBarcode promotes the rapid acquisition of biological species DNA sequence data that meet global standards by providing specialized services, and provides useful tools that will make barcoding cheaper and faster in the biodiversity community such as standardization, depository, management, and analysis of DNA barcode data. The system can be downloaded upon request, and an exemplary server has been constructed with which to build an Asian biodiversity system http://www.asianbarcode.org. PMID:19958506

2009-01-01

63

Amerindian mitochondrial DNA haplogroups predominate in the population of Argentina: towards a first nationwide forensic mitochondrial DNA sequence database.  

PubMed

The study presents South American mitochondrial DNA (mtDNA) data from selected north (N = 98), central (N = 193) and south (N = 47) Argentinean populations. Sequence analysis of the complete mtDNA control region (CR, 16024-576) resulted in 288 unique haplotypes ignoring C-insertions around positions 16193, 309, and 573; the additional analysis of coding region single nucleotide polymorphisms enabled a fine classification of the described lineages. The Amerindian haplogroups were most frequent in the north and south representing more than 60% of the sequences. A slightly different situation was observed in central Argentina where the Amerindian haplogroups represented less than 50%, and the European contribution was more relevant. Particular clades of the Amerindian subhaplogroups turned out to be nearly region-specific. A minor contribution of African lineages was observed throughout the country. This comprehensive admixture of worldwide mtDNA lineages and the regional specificity of certain clades in the Argentinean population underscore the necessity of carefully selecting regional samples in order to develop a nationwide mtDNA database for forensic and anthropological purposes. The mtDNA sequencing and analysis were performed under EMPOP guidelines in order to attain high quality for the mtDNA database. PMID:19680675

Bobillo, Maria Cecilia; Zimmermann, Bettina; Sala, Andrea; Huber, Gabriela; Röck, Alexander; Bandelt, Hans-Jürgen; Corach, Daniel; Parson, Walther

2010-07-01

64

The Lactamase Engineering Database: a critical survey of TEM sequences in public databases  

PubMed Central

Background TEM ?-lactamases are the main cause for resistance against ?-lactam antibiotics. Sequence information about TEM ?-lactamases is mainly found in the NCBI peptide database and TEM mutation table at . While the TEM mutation table is manually curated by experts in the lactamase field, who guarantee reliable and consistent information, the rapidly growing sequence and annotation information from the NCBI peptide database is sometimes inconsistent. Therefore, the Lactamase Engineering Database has been developed to collect the TEM ?-lactamase sequences from the NCBI peptide database and the TEM mutation table, systematically compare sequence information and naming, identify inconsistencies, and thus provide a versatile tool for reconciliation of data and for an investigation of the sequence-function relationship. Description The LacED currently provides 2399 sequence entries and 37 structure entries. Sequence information on 150 different TEM ?-lactamases was derived from the TEM mutation table which provides a unique number to each protein classified as TEM ?-lactamase. 293 TEM-like proteins were found in the NCBI protein database, but only 113 TEM ?-lactamase were common to both data sets. The 180 TEM ?-lactamases from the NCBI protein database which have not yet been assigned to a TEM number fall in three classes: (1) 89 proteins from microbial organisms and 35 proteins from cloning or expression vectors had a new mutation profile; (2) 55 proteins had inconsistent annotation in terms of TEM assignment or reported mutation profile; (3) 39 proteins are fragments. The LacED is web accessible at and contains multisequence alignments, structure information and reconciled annotation of TEM ?-lactamases. The LacED is weekly updated and supplies all data for download. Conclusion The Lactamase Engineering Database enables a systematic analysis of TEM ?-lactamase sequence and annotation data from different data sources, and thus provides a valuable tool to identify inconsistencies in sequences from the NCBI peptide database, to detect TEM ?-lactamases with a novel mutation profile, and to identify new amino acid positions at which mutations can occur. PMID:19698099

Thai, Quan Ke; Bos, Fabian; Pleiss, Jurgen

2009-01-01

65

DNA -- Intimate Information or Trash for Public Consumption?  

E-print Network

This essay discusses the increasingly popular police practice of covertly collecting DNA samples from people who inadvertently leave saliva, hair or other biological matter in public places. The essay contends that although the United States Supreme...

Wilson, Melanie D.

2008-01-01

66

Flexible and Publicly Verifiable Aggregation Query for Outsourced Databases in Cloud  

E-print Network

investigates this challenging problem and proposes an efficient publicly verifiable aggregation query schemeFlexible and Publicly Verifiable Aggregation Query for Outsourced Databases in Cloud Jiawei Yuan to design a client-verifiable (or publicly verifiable) aggregation query scheme that supports more flexible

67

76 FR 53912 - FDA's Public Database of Products With Orphan-Drug Designation: Replacing Non-Informative Code...  

Federal Register 2010, 2011, 2012, 2013

...FDA-2011-N-0607] FDA's Public Database of Products With Orphan-Drug Designation...descriptive identifiers on its public database of products that have received orphan-drug...designation were published on our public database with non-informative code names....

2011-08-30

68

Proposals to Regulate the Public's Rights to Use Information Stored in Databases  

NSDL National Science Digital Library

One of the items on the agenda for the 1996 World Intellectual Property Organization (WIPO) Diplomatic Conference (December 2-20 1996), is a database treaty that would effect the way databases are treated in terms of intellectual property. The proposed treaty "seeks to safeguard makers of databases against misappropriation of the fruits of their financial and professional investment in collecting, verifying and presenting the contents of databases. It does this by proposing protection that covers the whole or substantial parts of a database against certain acts by a user or by a competitor, for the limited duration of the right." Some have interpreted this to mean that the facts in the databases will become the intellectual property of the creators of the databases, a development that will have important consequences. Interested Internauts can decide for themselves by reading the treaty and a selection of responses that have been posted at public-domain.org.

1996-01-01

69

A New Passenger Support System for Public Transport using Mobile Database Access  

Microsoft Academic Search

We have been developing a mobile passenger support system for public transport. Passen- gers can make their travel plans and purchase necessary tickets by accessing databases via the system. After starting the travel, a mo- bile terminal checks the travel schedule of its user by accessing several databases and gath- ering various kinds of information. In this ap- plication field,

Koichi Goto; Yahiko Kambayashi

2002-01-01

70

A publication database for optical long baseline interferometry  

Microsoft Academic Search

Optical long baseline interferometry is a technique that has generated almost 850 refereed papers to date. The targets span a large variety of objects from planetary systems to extragalactic studies and all branches of stellar physics. We have created a database hosted by the JMMC and connected to the Optical Long Baseline Interferometry Newsletter (OLBIN) web site using MySQL and

Fabien Malbet; Guillaume Mella; Peter Lawson; Esther Taillifet; Sylvain Lafrasse

2010-01-01

71

75 FR 76831 - Publicly Available Consumer Product Safety Information Database  

Federal Register 2010, 2011, 2012, 2013

...should not create section 15 reporting obligations. The...consideration in section 15 cases and, therefore, we will...rate will increase in the case of the Database; currently...comments as reports of harm (15,140 reports of harm x...

2010-12-09

72

ArrayExpress - a public database of microarray experiments and gene expression profiles  

Microsoft Academic Search

ArrayExpress is a public database for high through- put functional genomics data. ArrayExpress con- sists of two parts—the ArrayExpress Repository, which is a MIAME supportive public archive of micro- array data, and the ArrayExpress Data Warehouse, which is a database of gene expression profiles selected from the repository and consistently re- annotated. Archived experiments can be queried by experiment attributes,

Helen E. Parkinson; Misha Kapushesky; Mohammadreza Shojatalab; Niran Abeygunawardena; R. Coulson; Anna Farne; Ele Holloway; N. Kolesnykov; P. Lilja; M. Lukk; R. Mani; Tim Rayner; Anjan Sharma; E. William; Ugis Sarkans; Alvis Brazma

2007-01-01

73

Common mitochondrial DNA haplogroups observed in an argentine population database sample  

Microsoft Academic Search

Mitochondrial DNA hypervariable regions I and II were sequenced from 403 unrelated Argentine individuals. The aim of this study was to create a population database as well as to identify the population diversity for this genetic marker by classifying it into haplogroups.The sequence polymorphisms of the HVI and HVII regions were determined by PCR and direct sequencing. The haplotypes found

Laura Catelli; Carola Romanini; Alicia Borosky; Mercedes Salado Puerto; Lourdes Prieto; Carlos Vullo

2009-01-01

74

More for the same? Enhancing the investigative potential of forensic DNA databases (REF 0415)  

Microsoft Academic Search

The UK has had a National DNA Database [NDNAD] since 1995. It now contains more than 4.5 million records representing 7.5% of the UK population. The Forensic Science Service has introduced two additional services designed to supplement and enhance the ability of law enforcement agencies to investigate offences. Both employ novel and bespoke software that exploit data held on the

Susan Pope; Timothy Clayton; Jonathan Whitaker; John Lowe; Roberto Puch-Solis

2009-01-01

75

Using the ADS Database to Study Trends in Astronomical Publication  

Microsoft Academic Search

The sociology of astronomical publication has traditionally been studied by looking for publication trends using every paper published in a few selected journals within a few selected years. For example, Abt (1981, PASP, 93, 269) examined the papers published in ApJ, ApJS, AJ, and PASP during the first year of each decade from 1910 to 1980. By analyzing the NASA

E. Schulman; A. L. Powell; J. C. French; G. Eichhorn; M. J. Kurtz; S. S. Murray

1996-01-01

76

Prisoners' expectations of the national forensic DNA database: surveillance and reconfiguration of individual rights.  

PubMed

In this paper we aim to discuss how Portuguese prisoners know and what they feel about surveillance mechanisms related to the inclusion and deletion of the DNA profiles of convicted criminals in the national forensic database. Through a set of interviews with individuals currently imprisoned we focus on the ways this group perceives forensic DNA technologies. While the institutional and political discourses maintain that the restricted use and application of DNA profiles within the national forensic database protects individuals' rights, the prisoners claim that police misuse of such technologies potentially makes it difficult to escape from surveillance and acts as a mean of reinforcing the stigma of delinquency. The prisoners also argue that additional intensive and extensive use of surveillance devices might be more protective of their own individual rights and might possibly increase potential for exoneration. PMID:21414735

Machado, Helena; Santos, Filipe; Silva, Susana

2011-07-15

77

MethylomeDB: a database of DNA methylation profiles of the brain  

PubMed Central

MethylomeDB (http://epigenomics.columbia.edu/methylomedb/index.html) is a new database containing genome-wide brain DNA methylation profiles. DNA methylation is an important epigenetic mark in the mammalian brain. In human studies, aberrant DNA methylation alterations have been associated with various neurodevelopmental and neuropsychiatric disorders such as schizophrenia, and depression. In this database, we present methylation profiles of carefully selected non-psychiatric control, schizophrenia, and depression samples. We also include data on one mouse forebrain sample specimen to allow for cross-species comparisons. In addition to our DNA methylation data generated in-house, we have and will continue to include published DNA methylation data from other research groups with the focus on brain development and function. Users can view the methylation data at single-CpG resolution with the option of wiggle and microarray formats. They can also download methylation data for individual samples. MethylomeDB offers an important resource for research into brain function and behavior. It provides the first source of comprehensive brain methylome data, encompassing whole-genome DNA methylation profiles of human and mouse brain specimens that facilitate cross-species comparative epigenomic investigations, as well as investigations of schizophrenia and depression methylomes. PMID:22140101

Xin, Yurong; Chanrion, Benjamin; O'Donnell, Anne H.; Milekic, Maria; Costa, Ramiro; Ge, Yongchao; Haghighi, Fatemeh G.

2012-01-01

78

Launching the Greek forensic DNA database. The legal framework and arising ethical issues.  

PubMed

Since the creation of the first national DNA database in Europe in 1995, many European countries have legislated laws for initiating and regulating their own databases. The Greek government legislated a law in 2008, by which the National DNA Database of Greece was founded and regulated. According to this law, only DNA profiles from convicted criminals were recorded. Nevertheless, a year later, in 2009, the law was amended to permit the creation of an expanded database including innocent people and children. Unfortunately, the new law is very vague in many aspects and does not respect the principle of proportionality. Therefore, according to our opinion, it will soon need to be re-amended. Furthermore, prior to legislating the new law, there was no debate with the community itself in order to clarify what system would best suit Greece and what the citizens would be willing to accept. We present the current legal framework in Greece, we highlight issues that need to be clarified and we discuss possible ethical issues that may arise. PMID:20851698

Voultsos, Polychronis; Njau, Samuel; Tairis, Nikolaos; Psaroulis, Dimitrios; Kovatsi, Leda

2011-11-01

79

Literature curation of protein interactions: measuring agreement across major public databases  

PubMed Central

Literature curation of protein interaction data faces a number of challenges. Although curators increasingly adhere to standard data representations, the data that various databases actually record from the same published information may differ significantly. Some of the reasons underlying these differences are well known, but their global impact on the interactions collectively curated by major public databases has not been evaluated. Here we quantify the agreement between curated interactions from 15?471 publications shared across nine major public databases. Results show that on average, two databases fully agree on 42% of the interactions and 62% of the proteins curated from the same publication. Furthermore, a sizable fraction of the measured differences can be attributed to divergent assignments of organism or splice isoforms, different organism focus and alternative representations of multi-protein complexes. Our findings highlight the impact of divergent curation policies across databases, and should be relevant to both curators and data consumers interested in analyzing protein-interaction data generated by the scientific community. Database URL: http://wodaklab.org/iRefWeb PMID:21183497

Turinsky, Andrei L.; Razick, Sabry; Turner, Brian; Wodak, Shoshana J.

2010-01-01

80

A perspective of publicly accessible/open-access chemistry databases.  

PubMed

The Internet has spawned access to unprecedented levels of information. For chemists the increasing number of resources they can use to access chemistry-related information provides them a valuable path to discovery of information, one which was previously limited to commercial and therefore constrained resources. The diversity of information continues to expand at a dramatic rate and, coupled with an increasing awareness for quality, curation and improved tools for focused searches, chemists are now able to find valuable information within a few seconds using a few keystrokes. This shift to publicly available resources offers great promise to the benefits of science and society yet brings with it increasing concern from commercial entities. This article will discuss the benefits and disruptions associated with an increase in publicly available scientific resources. PMID:18549975

Williams, Antony J

2008-06-01

81

DNA variant databases improve test accuracy and phenotype prediction in Alport syndrome.  

PubMed

X-linked Alport syndrome is a form of progressive renal failure caused by pathogenic variants in the COL4A5 gene. More than 700 variants have been described and a further 400 are estimated to be known to individual laboratories but are unpublished. The major genetic testing laboratories for X-linked Alport syndrome worldwide have established a Web-based database for published and unpublished COL4A5 variants ( https://grenada.lumc.nl/LOVD2/COL4A/home.php?select_db=COL4A5 ). This conforms with the recommendations of the Human Variome Project: it uses the Leiden Open Variation Database (LOVD) format, describes variants according to the human reference sequence with standardized nomenclature, indicates likely pathogenicity and associated clinical features, and credits the submitting laboratory. The database includes non-pathogenic and recurrent variants, and is linked to another COL4A5 mutation database and relevant bioinformatics sites. Access is free. Increasing the number of COL4A5 variants in the public domain helps patients, diagnostic laboratories, clinicians, and researchers. The database improves the accuracy and efficiency of genetic testing because its variants are already categorized for pathogenicity. The description of further COL4A5 variants and clinical associations will improve our ability to predict phenotype and our understanding of collagen IV biochemistry. The database for X-linked Alport syndrome represents a model for databases in other inherited renal diseases. PMID:23720012

Savige, Judy; Ars, Elisabet; Cotton, Richard G H; Crockett, David; Dagher, Hayat; Deltas, Constantinos; Ding, Jie; Flinter, Frances; Pont-Kingdon, Genevieve; Smaoui, Nizar; Torra, Roser; Storey, Helen

2014-06-01

82

The annotation and the usage of scientific databases could be improved with public issue tracker software  

PubMed Central

Since the publication of their longtime predecessor The Atlas of Protein Sequences and Structures in 1965 by Margaret Dayhoff, scientific databases have become a key factor in the organization of modern science. All the information and knowledge described in the novel scientific literature is translated into entries in many different scientific databases, making it possible to obtain very accurate information on a biological entity like genes or proteins without having to manually review the literature on it. However, even for the databases with the finest annotation procedures, errors or unclear parts sometimes appear in the publicly released version and influence the research of unaware scientists using them. The researcher that finds an error in a database is often left in a uncertain state, and often abandons the effort of reporting it because of a lack of a standard procedure to do so. In the present work, we propose that the simple adoption of a public error tracker application, as in many open software projects, could improve the quality of the annotations in many databases and encourage feedback from the scientific community on the data annotated publicly. In order to illustrate the situation, we describe a series of errors that we found and helped solve on the genes of a very well-known pathway in various biomedically relevant databases. We would like to show that, even if a majority of the most important scientific databases have procedures for reporting errors, these are usually not publicly visible, making the process of reporting errors time consuming and not useful. Also, the effort made by the user that reports the error often goes unacknowledged, putting him in a discouraging position. PMID:21186182

Dall'Olio, Giovanni Marco; Bertranpetit, Jaume; Laayouni, Hafid

2010-01-01

83

"Would you accept having your DNA profile inserted in the National Forensic DNA database? Why?" Results of a questionnaire applied in Portugal.  

PubMed

The creation and expansion of forensic DNA databases might involve potential threats to the protection of a range of human rights. At the same time, such databases have social benefits. Based on data collected through an online questionnaire applied to 628 individuals in Portugal, this paper aims to analyze the citizens' willingness to donate voluntarily a sample for profiling and inclusion in the National Forensic DNA Database and the views underpinning such a decision. Nearly one-quarter of the respondents would indicate 'no', and this negative response increased significantly with age and education. The overriding willingness to accept the inclusion of the individual genetic profile indicates an acknowledgement of the investigative potential of forensic DNA technologies and a relegation of civil liberties and human rights to the background, owing to the perceived benefits of protecting both society and the individual from crime. This rationale is mostly expressed by the idea that all citizens should contribute to the expansion of the National Forensic DNA Database for reasons that range from the more abstract assumption that donating a sample for profiling would be helpful in fighting crime to the more concrete suggestion that everyone (criminals and non-criminals) should be in the database. The concerns with the risks of accepting the donation of a sample for genetic profiling and inclusion in the National Forensic DNA Database are mostly related to lack of control and insufficient or unclear regulations concerning safeguarding individuals' data and supervising the access and uses of genetic data. By providing an empirically-grounded understanding of the attitudes regarding willingness to donate voluntary a sample for profiling and inclusion in a National Forensic DNA Database, this study also considers the citizens' perceived benefits and risks of operating forensic DNA databases. These collective views might be useful for the formation of international common ethical standards for the development and governance of DNA databases in a framework in which the citizens' perspectives are taken into consideration. PMID:24315600

Machado, Helena; Silva, Susana

2014-01-01

84

Harp: a distributed query system for legacy public libraries and structured databases  

Microsoft Academic Search

The main purpose of a digital library is to facilitate users easy access to enormous amount of globally networked information. Typically, this information includes preexisting public library catalog data, digitized document collections, and other databases. In this article, we describe the distributed query system of a digital library prototype system known as HARP. In the HARP project, we have designed

Ee-Peng Lim; Ying Lu

1999-01-01

85

Towards a public analysis database for LHC new physics searches using MadAnalysis 5  

E-print Network

We present the implementation, in the MadAnalysis 5 framework, of several ATLAS and CMS searches for supersymmetry in data recorded during the first run of the LHC. We provide extensive details on the validation of our implementations and propose to create a public analysis database within this framework.

B. Dumont; B. Fuks; S. Kraml; S. Bein; G. Chalons; E. Conte; S. Kulkarni; D. Sengupta; C. Wymant

2014-07-11

86

Estimating haplotype frequencies by combining data from large DNA pools with database information.  

PubMed

We assume that allele frequency data have been extracted from several large DNA pools, each containing genetic material of up to hundreds of sampled individuals. Our goal is to estimate the haplotype frequencies among the sampled individuals by combining the pooled allele frequency data with prior knowledge about the set of possible haplotypes. Such prior information can be obtained, for example, from a database such as HapMap. We present a Bayesian haplotyping method for pooled DNA based on a continuous approximation of the multinomial distribution. The proposed method is applicable when the sizes of the DNA pools and/or the number of considered loci exceed the limits of several earlier methods. In the example analyses, the proposed model clearly outperforms a deterministic greedy algorithm on real data from the HapMap database. With a small number of loci, the performance of the proposed method is similar to that of an EM-algorithm, which uses a multinormal approximation for the pooled allele frequencies, but which does not utilize prior information about the haplotypes. The method has been implemented using Matlab and the code is available upon request from the authors. PMID:21071795

Gasbarra, Dario; Kulathinal, Sangita; Pirinen, Matti; Sillanpää, Mikko J

2011-01-01

87

Feline Non-repetitive Mitochondrial DNA Control Region Database for Forensic Evidence  

PubMed Central

The domestic cat is the one of the most popular pets throughout the world. A by-product of owning, interacting with, or being in a household with a cat is the transfer of shed fur to clothing or personal objects. As trace evidence, transferred cat fur is a relatively untapped resource for forensic scientists. Both phenotypic and genotypic characteristics can be obtained from cat fur, but databases for neither aspect exist. Because cats incessantly groom, cat fur may have nucleated cells, not only in the hair bulb, but also as epithelial cells on the hair shaft deposited during the grooming process, thereby generally providing material for DNA profiling. To effectively exploit cat hair as a resource, representative databases must be established. This study evaluates 402 bp of the mtDNA control region (CR) from 1,394 cats, including cats from 25 distinct worldwide populations and 26 breeds. Eighty-three percent of the cats are represented by 12 major mitotypes. An additional 8.0% are clearly derived from the major mitotypes. Unique sequences were found in 7.5% of the cats. The overall genetic diversity for this data set was 0.8813 ± 0.0046 with a random match probability of 11.8%. This region of the cat mtDNA has discriminatory power suitable for forensic application worldwide. PMID:20457082

Grahn, R. A.; Kurushima, J. D.; Billings, N. C.; Grahn, J.C.; Halverson, J. L.; Hammer, E.; Ho, C.K.; Kun, T. J.; Levy, J.K.; Lipinski, M. J.; Mwenda, J.M.; Ozpinar, H.; Schuster, R.K; Shoorijeh, S.J.; Tarditi, C. R.; Waly, N.E.; Wictum, E. J.; Lyons, L. A.

2010-01-01

88

Feline non-repetitive mitochondrial DNA control region database for forensic evidence.  

PubMed

The domestic cat is the one of the most popular pets throughout the world. A by-product of owning, interacting with, or being in a household with a cat is the transfer of shed fur to clothing or personal objects. As trace evidence, transferred cat fur is a relatively untapped resource for forensic scientists. Both phenotypic and genotypic characteristics can be obtained from cat fur, but databases for neither aspect exist. Because cats incessantly groom, cat fur may have nucleated cells, not only in the hair bulb, but also as epithelial cells on the hair shaft deposited during the grooming process, thereby generally providing material for DNA profiling. To effectively exploit cat hair as a resource, representative databases must be established. The current study evaluates 402 bp of the mtDNA control region (CR) from 1394 cats, including cats from 25 distinct worldwide populations and 26 breeds. Eighty-three percent of the cats are represented by 12 major mitotypes. An additional 8.0% are clearly derived from the major mitotypes. Unique sequences are found in 7.5% of the cats. The overall genetic diversity for this data set is 0.8813±0.0046 with a random match probability of 11.8%. This region of the cat mtDNA has discriminatory power suitable for forensic application worldwide. PMID:20457082

Grahn, R A; Kurushima, J D; Billings, N C; Grahn, J C; Halverson, J L; Hammer, E; Ho, C K; Kun, T J; Levy, J K; Lipinski, M J; Mwenda, J M; Ozpinar, H; Schuster, R K; Shoorijeh, S J; Tarditi, C R; Waly, N E; Wictum, E J; Lyons, L A

2011-01-01

89

76 FR 77533 - Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single...  

Federal Register 2010, 2011, 2012, 2013

...2011-N-13] Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single-Family Securitized Loan...FHFA's adoption of an Order revising FHFA's Public Use Database matrices to include certain data fields for high-cost...

2011-12-13

90

A PCR multiplex and database for forensic DNA identification of dogs.  

PubMed

Animal-derived trace evidence is a common finding at crime scenes and may provide an important link between victim(s) and suspect(s). A database of 558 dogs of pure and mixed breeds is described and analyzed with two PCR multiplexes of 17 microsatellites. Summary statistics (number of alleles, expected and observed heterozygosity and power of exclusion) are compared between breeds. Marked population substructure in dog breeds indicates significant inbreeding, and the use of a conservative theta value is recommended in likelihood calculations for determining the significance of a DNA match. Evidence is presented that the informativeness of the canine microsatellites, despite inbreeding, is comparable to the human CODIS loci. Two cases utilizing canine DNA typing, State of Washington v. Kenneth Leuluaialii and George Tuilefano and Crown v. Daniel McGowan, illustrate the potential of canine microsatellite markers for forensic investigations. PMID:15813546

Halverson, Joy; Basten, Christopher

2005-03-01

91

DNA Identification of Mountain Lions Involved in Livestock Predation and Public Safety Incidents and Investigations  

E-print Network

1 DNA Identification of Mountain Lions Involved in Livestock Predation and Public Safety Incidents concolor, bobcat, forensic, genetics, DNA techniques, noninvasive sampling, fecal DNA, prey swab DNA ABSTRACT Using three case studies, we demonstrated the utility of techniques to analyze DNA from trace

Ernest, Holly

92

Genomics and Public Health Research: Can the State Allow Access to Genomic Databases?  

PubMed Central

Because many diseases are multifactorial disorders, the scientific progress in genomics and genetics should be taken into consideration in public health research. In this context, genomic databases will constitute an important source of information. Consequently, it is important to identify and characterize the State’s role and authority on matters related to public health, in order to verify whether it has access to such databases while engaging in public health genomic research. We first consider the evolution of the concept of public health, as well as its core functions, using a comparative approach (e.g. WHO, PAHO, CDC and the Canadian province of Quebec). Following an analysis of relevant Quebec legislation, the precautionary principle is examined as a possible avenue to justify State access to and use of genomic databases for research purposes. Finally, we consider the Influenza pandemic plans developed by WHO, Canada, and Quebec, as examples of key tools framing public health decision-making process. We observed that State powers in public health, are not, in Quebec, well adapted to the expansion of genomics research. We propose that the scope of the concept of research in public health should be clear and include the following characteristics: a commitment to the health and well-being of the population and to their determinants; the inclusion of both applied research and basic research; and, an appropriate model of governance (authorization, follow-up, consent, etc.). We also suggest that the strategic approach version of the precautionary principle could guide collective choices in these matters. PMID:23113174

Cousineau, J; Girard, N; Monardes, C; Leroux, T; Jean, M Stanton

2012-01-01

93

Accessing the public MIMIC-II intensive care relational database for clinical research  

PubMed Central

Background The Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database is a free, public resource for intensive care research. The database was officially released in 2006, and has attracted a growing number of researchers in academia and industry. We present the two major software tools that facilitate accessing the relational database: the web-based QueryBuilder and a downloadable virtual machine (VM) image. Results QueryBuilder and the MIMIC-II VM have been developed successfully and are freely available to MIMIC-II users. Simple example SQL queries and the resulting data are presented. Clinical studies pertaining to acute kidney injury and prediction of fluid requirements in the intensive care unit are shown as typical examples of research performed with MIMIC-II. In addition, MIMIC-II has also provided data for annual PhysioNet/Computing in Cardiology Challenges, including the 2012 Challenge “Predicting mortality of ICU Patients”. Conclusions QueryBuilder is a web-based tool that provides easy access to MIMIC-II. For more computationally intensive queries, one can locally install a complete copy of MIMIC-II in a VM. Both publicly available tools provide the MIMIC-II research community with convenient querying interfaces and complement the value of the MIMIC-II relational database. PMID:23302652

2013-01-01

94

Addressing database mismatch in forensic speaker recognition with Ahumada III: a public real-casework database in Spanish  

Microsoft Academic Search

This paper presents and describes Ahumada III, a speech database in Spanish collected from real forensic cases. In i ts current release, the database presents male speakers recorded using the systems and procedures followed by Spanish Guardia Civil police force. The paper also explores the usefulness of such a corpus for facing the important problem of database mis- match in

Daniel Ramos; Joaquin Gonzalez-Rodriguez; Javier Gonzalez-Dominguez; Jose Juan Lucena-Molina

2008-01-01

95

A large population genetic study of 15 autosomal short tandem repeat loci for establishment of Korean DNA profile database.  

PubMed

Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10(-17). This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications. PMID:21597912

Yoo, Seong Yeon; Cho, Nam Soo; Park, Myung Jin; Seong, Ki Min; Hwang, Jung Ho; Song, Seok Bean; Han, Myun Soo; Lee, Won Tae; Chung, Ki Wha

2011-07-01

96

Development and expansion of high-quality control region databases to improve forensic mtDNA evidence interpretation  

Microsoft Academic Search

In an effort to increase the quantity, breadth and availability of mtDNA databases suitable for forensic comparisons, we have developed a high-throughput process to generate approximately 5000 control region sequences per year from regional US populations, global populations from which the current US population is derived and global populations currently under-represented in available forensic databases. The system utilizes robotic instrumentation

Jodi A. Irwin; Jessica L. Saunier; Katharine M. Strouss; Kimberly A. Sturk; Toni M. Diegoli; Rebecca S. Just; Michael D. Coble; Walther Parson; Thomas J. Parsons

2007-01-01

97

Does an English appeal court ruling increase the risks of miscarriages of justice when complex DNA profiles are searched against the national DNA database?  

PubMed

Likelihood ratio (LR) methods to interpret multi-contributor, low template, complex DNA mixtures are becoming standard practice. The next major development will be to introduce search engines based on the new methods to interrogate very large national DNA databases, such as those held by China, the USA and the UK. Here we describe a rapid method that was used to assign a LR to each individual member of database of 5 million genotypes which can be ranked in order. Previous authors have only considered database trawls in the context of binary match or non-match criteria. However, the concept of match/non-match no longer applies within the new paradigm introduced, since the distribution of resultant LRs is continuous for practical purposes. An English appeal court decision allows scientists to routinely report complex DNA profiles using nothing more than their subjective personal 'experience of casework' and 'observations' in order to apply an expression of the rarity of an evidential sample. This ruling must be considered in context of a recent high profile English case, where an individual was extracted from a database and wrongly accused of a serious crime. In this case the DNA evidence was used to negate the overwhelming exculpatory (non-DNA) evidence. Demonstrable confirmation bias, also known as the 'CSI-effect, seriously affected the investigation. The case demonstrated that in practice, databases could be used to select and prosecute an individual, simply because he ranked high in the list of possible matches. We have identified this phenomenon as a cognitive error which we term: 'the naïve investigator effect'. We take the opportunity to test the performance of database extraction strategies either by using a simple matching allele count (MAC) method or LR. The example heard by the appeal court is used as the exemplar case. It is demonstrated that the LR search-method offers substantial benefits compared to searches based on simple matching allele count (MAC) methods. PMID:25151459

Gill, P; Bleka, O; Egeland, T

2014-11-01

98

Forensic genetic analysis of mitochondrial DNA hypervariable region I/II sequences: an expanded Korean population database.  

PubMed

We have analyzed variation of the mitochondrial DNA (mtDNA) hypervariable segments I and II (HVS-I and HVS-II) in 185 randomly chosen individuals from Korea to provide an expanded and reliable Korean database. Combined sequence comparison of HVS-I and HVS-II led to the identification of 167 different haplotypes characterized by 154 variable sites. One hundred and fifty-one of the haplotypes were individual-specific, 14 were found in two individuals and 2 were found in three individuals. A pairwise comparison of the 185 HVS-I/II sequences found an average of 10.11 +/- 4.63 differences between individuals. The random match probability and gene diversity for the combined hypervariable regions were estimated at 0.66% and 0.9988, respectively. Analyzing the expanded database including three previously reported data sets and the present data using haplogroup-based comparisons and comparison with closely related sequences allowed errors to be detected and eliminated, thus considerably improving data quality. Sample division comparisons based on PhiST genetic distance measures revealed no significant population differentiation in the distribution of mtDNA sequence variations between the present data set and a database in The Scientific Working Group on DNA Analysis Methods (SWGDAM), but did indicate differences from other sets of data. Based on the results of mtDNA profiles, almost all of the mtDNA types studied here could be classified into subsets of haplogroups common in east Asia, and show that the Koreans possess lineages from both the southern and the northern haplogroup complexes of east Asian populations. The new data, combined with other mtDNA sequences, demonstrate how useful comparison with closely related mtDNA sequences can be for improving database quality, as well as providing haplotype information for forensic and population genetic analyses in the Korean population. PMID:15990264

Jin, Han Jun; Kwak, Kyoung Don; Hong, Seung Bum; Shin, Dong Jik; Han, Myun Soo; Tyler-Smith, Chris; Kim, Wook

2006-05-10

99

A spatial national health facility database for public health sector planning in Kenya in 2008  

PubMed Central

Background Efforts to tackle the enormous burden of ill-health in low-income countries are hampered by weak health information infrastructures that do not support appropriate planning and resource allocation. For health information systems to function well, a reliable inventory of health service providers is critical. The spatial referencing of service providers to allow their representation in a geographic information system is vital if the full planning potential of such data is to be realized. Methods A disparate series of contemporary lists of health service providers were used to update a public health facility database of Kenya last compiled in 2003. These new lists were derived primarily through the national distribution of antimalarial and antiretroviral commodities since 2006. A combination of methods, including global positioning systems, was used to map service providers. These spatially-referenced data were combined with high-resolution population maps to analyze disparity in geographic access to public health care. Findings The updated 2008 database contained 5,334 public health facilities (67% ministry of health; 28% mission and nongovernmental organizations; 2% local authorities; and 3% employers and other ministries). This represented an overall increase of 1,862 facilities compared to 2003. Most of the additional facilities belonged to the ministry of health (79%) and the majority were dispensaries (91%). 93% of the health facilities were spatially referenced, 38% using global positioning systems compared to 21% in 2003. 89% of the population was within 5 km Euclidean distance to a public health facility in 2008 compared to 71% in 2003. Over 80% of the population outside 5 km of public health service providers was in the sparsely settled pastoralist areas of the country. Conclusion We have shown that, with concerted effort, a relatively complete inventory of mapped health services is possible with enormous potential for improving planning. Expansion in public health care in Kenya has resulted in significant increases in geographic access although several areas of the country need further improvements. This information is key to future planning and with this paper we have released the digital spatial database in the public domain to assist the Kenyan Government and its partners in the health sector. PMID:19267903

Noor, Abdisalan M; Alegana, Victor A; Gething, Peter W; Snow, Robert W

2009-01-01

100

Dfam: a database of repetitive DNA based on profile hidden Markov models.  

PubMed

We present a database of repetitive DNA elements, called Dfam (http://dfam.janelia.org). Many genomes contain a large fraction of repetitive DNA, much of which is made up of remnants of transposable elements (TEs). Accurate annotation of TEs enables research into their biology and can shed light on the evolutionary processes that shape genomes. Identification and masking of TEs can also greatly simplify many downstream genome annotation and sequence analysis tasks. The commonly used TE annotation tools RepeatMasker and Censor depend on sequence homology search tools such as cross_match and BLAST variants, as well as Repbase, a collection of known TE families each represented by a single consensus sequence. Dfam contains entries corresponding to all Repbase TE entries for which instances have been found in the human genome. Each Dfam entry is represented by a profile hidden Markov model, built from alignments generated using RepeatMasker and Repbase. When used in conjunction with the hidden Markov model search tool nhmmer, Dfam produces a 2.9% increase in coverage over consensus sequence search methods on a large human benchmark, while maintaining low false discovery rates, and coverage of the full human genome is 54.5%. The website provides a collection of tools and data views to support improved TE curation and annotation efforts. Dfam is also available for download in flat file format or in the form of MySQL table dumps. PMID:23203985

Wheeler, Travis J; Clements, Jody; Eddy, Sean R; Hubley, Robert; Jones, Thomas A; Jurka, Jerzy; Smit, Arian F A; Finn, Robert D

2013-01-01

101

Similarity landscapes: An improved method for scientific visualization of information from protein and DNA database searches  

SciTech Connect

This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors have used computer simulations and examination of a variety of databases to answer questions about a wide range of evolutionary questions. The authors have found that there is a clear distinction in the evolution of HIV-1 and HIV-2, with the former and more virulent virus evolving more rapidly at a functional level. The authors have discovered highly non-random patterns in the evolution of HIV-1 that can be attributed to a variety of selective pressures. In the course of examination of microsatellite DNA (short repeat regions) in microorganisms, the authors have found clear differences between prokaryotes and eukaryotes in their distribution, differences that can be tied to different selective pressures. They have developed a new method (topiary pruning) for enhancing the phylogenetic information contained in DNA sequences. Most recently, the authors have discovered effects in complex rainforest ecosystems that indicate strong frequency-dependent interactions between host species and their parasites, leading to the maintenance of ecosystem variability.

Dogget, N.; Myers, G. [Los Alamos National Lab., NM (United States); Wills, C.J. [Univ. of California, San Diego, CA (United States)

1998-12-01

102

Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database.  

PubMed

Large forensic mtDNA databases which adhere to strict guidelines for generation and maintenance, are not available for many populations outside of the United States and western Europe. We have established a high quality mtDNA control region sequence database for urban Nairobi as both a reference database for forensic investigations, and as a tool to examine the genetic variation of Kenyan sequences in the context of known African variation. The Nairobi sequences exhibited high variation and a low random match probability, indicating utility for forensic testing. Haplogroup identification and frequencies were compared with those reported from other published studies on African, or African-origin populations from Mozambique, Sierra Leone, and the United States, and suggest significant differences in the mtDNA compositions of the various populations. The quality of the sequence data in our study was investigated and supported using phylogenetic measures. Our data demonstrate the diversity and distinctiveness of African populations, and underline the importance of establishing additional forensic mtDNA databases of indigenous African populations. PMID:15248073

Brandstätter, Anita; Peterson, Christine T; Irwin, Jodi A; Mpoke, Solomon; Koech, Davy K; Parson, Walther; Parsons, Thomas J

2004-10-01

103

Privacy issues with DNA databases and retention of individuals' DNA information by law enforcement agencies: the holding of the European Court of Human Rights case S and Marper v. United Kingdom should be adapted to American Fourth Amendment jurisprudence  

Microsoft Academic Search

When law enforcement agencies collect, retain, and use individuals' DNA information in DNA databases for crime prevention purposes the presumption of innocence is reduced for those individuals. Collection and use of DNA information has benefits, greatly assisting law enforcement agencies in their criminal investigations. However, problems arise when DNA information is retained and used for individuals who have been acquitted,

Michael Lwin

2010-01-01

104

Publicly available database for spectral line measurements of SDSS DR7 galaxies  

NASA Astrophysics Data System (ADS)

We present a new database of absorption and emission-line measurements based on the Sloan Digital Sky Survey (SDSS) 7th data release of galaxies within a redshift of 0.2. Using the publicly available penalized pixel-fitting (pPXF) and gas and absorption line fitting (gandalf) codes, our work improve the existing measurements for stellar kinematics, the strength of various absorption line features, and the flux and width of the emissions from different species of ionised gas. Most notable of our work is that, we provide quality of the fit to assess reliability of the measurements. The quality assessment can be highly effective for finding new classes of objects. For example, based on the quality assessment around the Ha and [NII] nebular lines, we found approximately 1% of the SDSS spectra which classified as galaxies by the SDSS pipeline are in fact type I Seyfert AGN. This paper presents a summary of the recent paper, Oh et al.(2011). The database is publicly available at http://gem.yonsei.ac.kr/ossy/.

Oh, Kyuseok; Sarzi, Marc; Schawinski, Kevin; Yi, Sukyoung K.

2012-08-01

105

Reusable data in public health data-bases-problems encountered in Danish Children's Database.  

PubMed

Denmark have unique health informatics databases e.g. "The Children's Database", which since 2009 holds data on all Danish children from birth until 17 years of age. In the current set-up a number of potential sources of errors exist - both technical and human-which means that the data is flawed. This gives rise to erroneous statistics and makes the data unsuitable for research purposes. In order to make the data usable, it is necessary to develop new methods for validating the data generation process at the municipal/regional/national level. In the present ongoing research project, two research areas are combined: Public Health Informatics and Computer Science, and both ethnographic as well as system engineering research methods are used. The project is expected to generate new generic methods and knowledge about electronic data collection and transmission in different social contexts and by different social groups and thus to be of international importance, since this is sparsely documented in the Public Health Informatics perspective. This paper presents the preliminary results, which indicate that health information technology used ought to be subject for redesign, where a thorough insight into the work practices should be point of departure. PMID:22874263

Høstgaard, Anna Marie; Pape-Haugaard, Louise

2012-01-01

106

DNA banking and DNA databanking: Legal, ethical, and public policy issues. Progress report, [April 1, 1993--March 31, 1994  

SciTech Connect

The purpose of the grant was to provide support to enable us to: (1) perform legal and empirical research and critically analyze DNA banking and DNA databanking as those activities are conducted by state forensic laboratories, the military, academic researchers, and commercial enterprises; and (2) develop a broadcast quality educational videotape for viewing by the general public about DNA technology and the privacy and related issues that it raises. The grant thus has both a research and analysis component and a public education component. This report outlines the work completed since the inception of the project and describes the activities still in progress.

Reilly, P.R.; McEwen, J.E.; Small, D.

1994-02-18

107

Kingston Frontenac Public Library's Online Database Collection Copied from the A-to-Z Database List; Updated July 14, 2014  

E-print Network

List; Updated July 14, 2014 Alt Health Watch This database focuses on the many perspectives to a collection of over 1,000 audiobooks, from Popular Fiction titles and Children's books to Non books, radio and television transcipts, and even photographs and video, are also provided for each topic

Abolmaesumi, Purang

108

Polymorphisms of mtDNA control region in Tunisian and Moroccan populations: An enrichment of forensic mtDNA databases with Northern Africa data  

Microsoft Academic Search

Current forensic mitochondrial (mt)DNA databases are limited in representative population data of African origin. We investigated HVS-I\\/HVS-II sequences of 120 Tunisian and Moroccan healthy male donors applying stringent quality criteria to assure high quality of the data and phylogenetic alignment and notation of the sequences. Among 64 Tunisians, 56 different haplotypes were observed and the most common haplotype (16187T 16189C

Chiara Turchi; Loredana Buscemi; Erika Giacchino; Valerio Onofri; Liane Fendt; Walther Parson; Adriano Tagliabracci

2009-01-01

109

Familial searching: a specialist forensic DNA profiling service utilising the National DNA Database to identify unknown offenders via their relatives--the UK experience.  

PubMed

The National DNA Database (NDNAD) of England and Wales was established on April 10th 1995. The NDNAD is governed by a variety of legislative instruments that mean that DNA samples can be taken if an individual is arrested and detained in a police station. The biological samples and the DNA profiles derived from them can be used for purposes related to the prevention and detection of crime, the investigation of an offence and for the conduct of a prosecution. Following the South East Asian Tsunami of December 2004, the legislation was amended to allow the use of the NDNAD to assist in the identification of a deceased person or of a body part where death has occurred from natural causes or from a natural disaster. The UK NDNAD now contains the DNA profiles of approximately 6 million individuals representing 9.6% of the UK population. As the science of DNA profiling advanced, the National DNA Database provided a potential resource for increased intelligence beyond the direct matching for which it was originally created. The familial searching service offered to the police by several UK forensic science providers exploits the size and geographic coverage of the NDNAD and the fact that close relatives of an offender may share a significant proportion of that offender's DNA profile and will often reside in close geographic proximity to him or her. Between 2002 and 2011 Forensic Science Service Ltd. (FSS) provided familial search services to support 188 police investigations, 70 of which are still active cases. This technique, which may be used in serious crime cases or in 'cold case' reviews when there are few or no investigative leads, has led to the identification of 41 perpetrators or suspects. In this paper we discuss the processes, utility, and governance of the familial search service in which the NDNAD is searched for close genetic relatives of an offender who has left DNA evidence at a crime scene, but whose DNA profile is not represented within the NDNAD. We discuss the scientific basis of the familial search approach, other DNA-based methods for eliminating individuals from the candidate lists generated by these NDNAD searches, the value of filtering these lists by age, ethnic appearance and geography and the governance required by the NDNAD Strategy Board when a police force commissions a familial search. We present the FSS data in relation to the utility of the familial searching service and demonstrate the power of the technique by reference to casework examples. We comment on the uptake of familial searching of DNA databases in the USA, the Netherlands, Australia, and New Zealand. Finally, following the adverse ruling by the European Court of Human Rights against the UK in regard to the S & Marper cases and the consequent introduction of the Protection of Freedoms Act (2012), we discuss the impact that changes to regulations concerning the storage of DNA samples will have on the continuing provision of familial searching of the National DNA Database in England and Wales. PMID:24315582

Maguire, C N; McCallum, L A; Storey, C; Whitaker, J P

2014-01-01

110

Amerindian mitochondrial DNA haplogroups predominate in the population of Argentina: towards a first nationwide forensic mitochondrial DNA sequence database  

Microsoft Academic Search

The study presents South American mitochondrial DNA (mtDNA) data from selected north (N?=?98), central (N?=?193) and south (N?=?47) Argentinean populations. Sequence analysis of the complete mtDNA control region (CR, 16024–576) resulted in 288 unique\\u000a haplotypes ignoring C-insertions around positions 16193, 309, and 573; the additional analysis of coding region single nucleotide\\u000a polymorphisms enabled a fine classification of the described lineages.

Maria Cecilia Bobillo; Bettina Zimmermann; Andrea Sala; Gabriela Huber; Alexander Röck; Hans-Jürgen Bandelt; Daniel Corach; Walther Parson

2010-01-01

111

Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics  

PubMed Central

We report 80,388 ESTs from 23 Atlantic salmon (Salmo salar) cDNA libraries (61,819 ESTs), 6 rainbow trout (Oncorhynchus mykiss) cDNA libraries (14,544 ESTs), 2 chinook salmon (Oncorhynchus tshawytscha) cDNA libraries (1317 ESTs), 2 sockeye salmon (Oncorhynchus nerka) cDNA libraries (1243 ESTs), and 2 lake whitefish (Coregonus clupeaformis) cDNA libraries (1465 ESTs). The majority of these are 3? sequences, allowing discrimination between paralogs arising from a recent genome duplication in the salmonid lineage. Sequence assembly reveals 28,710 different S. salar, 8981 O. mykiss, 1085 O. tshawytscha, 520 O. nerka, and 1176 C. clupeaformis putative transcripts. We annotate the submitted portion of our EST database by molecular function. Higher- and lower-molecular-weight fractions of libraries are shown to contain distinct gene sets, and higher rates of gene discovery are associated with higher-molecular weight libraries. Pyloric caecum library group annotations indicate this organ may function in redox control and as a barrier against systemic uptake of xenobiotics. A microarray is described, containing 7356 salmonid elements representing 3557 different cDNAs. Analyses of cross-species hybridizations to this cDNA microarray indicate that this resource may be used for studies involving all salmonids. PMID:14962987

Rise, Matthew L.; von Schalburg, Kristian R.; Brown, Gordon D.; Mawer, Melanie A.; Devlin, Robert H.; Kuipers, Nathanael; Busby, Maura; Beetz-Sargent, Marianne; Alberto, Roberto; Gibbs, A. Ross; Hunt, Peter; Shukin, Robert; Zeznik, Jeffrey A.; Nelson, Colleen; Jones, Simon R.M.; Smailus, Duane E.; Jones, Steven J.M.; Schein, Jacqueline E.; Marra, Marco A.; Butterfield, Yaron S.N.; Stott, Jeff M.; Ng, Siemon H.S.; Davidson, William S.; Koop, Ben F.

2004-01-01

112

Mitochondrial DNA in the Central European population. Human identification with the help of the forensic mt-DNA D-loop-base database.  

PubMed

Sequencing of mtDNA is an advanced method for the individualisation of traces. Disadvantages of this method are expensive and time-consuming analysis and evaluation procedures as well as the necessary stock of population-genetic data which is still insufficient. Central European institutes of forensic medicine from Germany, Austria, and Switzerland have been working together since the beginning of 1998 to establish a mtDNA database. The aim is to build up a large stock of forensically established data and provide population-genetic data for frequency investigations, which will serve as a basis for expert opinions and scientific research. Good data quality is ensured by using original sequences only. Ring tests, which have been conducted to enhance analytical reliability, revealed a high correspondence rate of the analytical results obtained by the individual member institutes. Today 1410 sequences are available for comparison, of which 1285 sequences in the HV1 and HV2 regions cover the full ranges from 16051 to 16365 and from 73 to 340 (according to Anderson). The major part is formed by Central European sequences comprising 1256 data sets from Germany, Austria, and Switzerland. Today the database contains sequences from a total of 12 European, six African and three Asian countries including 100 sequences from Japan. This paper is aimed at discussing the individualisation potentials of mtDNA as well as the possibilities and limits of ethnic differentiation by means of pairwise sequence differences on the basis of the data stock available. PMID:10978611

Wittig, H; Augustin, C; Baasner, A; Bulnheim, U; Dimo-Simonin, N; Edelmann, J; Hering, S; Jung, S; Lutz, S; Michael, M; Parson, W; Poetsch, M; Schneider, P M; Weichhold, G; Krause, D

2000-09-11

113

DISTRIBUTED STRUCTURE-SEARCHABLE TOXICITY (DSSTOX) DATABASE NETWORK: MAKING PUBLIC TOXICITY DATA RESOURCES MORE ACCESSIBLE AND USABLE FOR DATA EXPLORATION AND SAR DEVELOPMENT  

EPA Science Inventory

Distributed Structure-Searchable Toxicity (DSSTox) Database Network: Making Public Toxicity Data Resources More Accessible and U sable for Data Exploration and SAR Development Many sources of public toxicity data are not currently linked to chemical structure, are not ...

114

Defining new criteria for selection of cell-based intestinal models using publicly available databases  

PubMed Central

Background The criteria for choosing relevant cell lines among a vast panel of available intestinal-derived lines exhibiting a wide range of functional properties are still ill-defined. The objective of this study was, therefore, to establish objective criteria for choosing relevant cell lines to assess their appropriateness as tumor models as well as for drug absorption studies. Results We made use of publicly available expression signatures and cell based functional assays to delineate differences between various intestinal colon carcinoma cell lines and normal intestinal epithelium. We have compared a panel of intestinal cell lines with patient-derived normal and tumor epithelium and classified them according to traits relating to oncogenic pathway activity, epithelial-mesenchymal transition (EMT) and stemness, migratory properties, proliferative activity, transporter expression profiles and chemosensitivity. For example, SW480 represent an EMT-high, migratory phenotype and scored highest in terms of signatures associated to worse overall survival and higher risk of recurrence based on patient derived databases. On the other hand, differentiated HT29 and T84 cells showed gene expression patterns closest to tumor bulk derived cells. Regarding drug absorption, we confirmed that differentiated Caco-2 cells are the model of choice for active uptake studies in the small intestine. Regarding chemosensitivity we were unable to confirm a recently proposed association of chemo-resistance with EMT traits. However, a novel signature was identified through mining of NCI60 GI50 values that allowed to rank the panel of intestinal cell lines according to their drug responsiveness to commonly used chemotherapeutics. Conclusions This study presents a straightforward strategy to exploit publicly available gene expression data to guide the choice of cell-based models. While this approach does not overcome the major limitations of such models, introducing a rank order of selected features may allow selecting model cell lines that are more adapted and pertinent to the addressed biological question. PMID:22726358

2012-01-01

115

Construction of a Public CHO Cell Line Transcript Database Using Versatile Bioinformatics Analysis Pipelines  

PubMed Central

Chinese hamster ovary (CHO) cell lines represent the most commonly used mammalian expression system for the production of therapeutic proteins. In this context, detailed knowledge of the CHO cell transcriptome might help to improve biotechnological processes conducted by specific cell lines. Nevertheless, very few assembled cDNA sequences of CHO cells were publicly released until recently, which puts a severe limitation on biotechnological research. Two extended annotation systems and web-based tools, one for browsing eukaryotic genomes (GenDBE) and one for viewing eukaryotic transcriptomes (SAMS), were established as the first step towards a publicly usable CHO cell genome/transcriptome analysis platform. This is complemented by the development of a new strategy to assemble the ca. 100 million reads, sequenced from a broad range of diverse transcripts, to a high quality CHO cell transcript set. The cDNA libraries were constructed from different CHO cell lines grown under various culture conditions and sequenced using Roche/454 and Illumina sequencing technologies in addition to sequencing reads from a previous study. Two pipelines to extend and improve the CHO cell line transcripts were established. First, de novo assemblies were carried out with the Trinity and Oases assemblers, using varying k-mer sizes. The resulting contigs were screened for potential CDS using ESTScan. Redundant contigs were filtered out using cd-hit-est. The remaining CDS contigs were re-assembled with CAP3. Second, a reference-based assembly with the TopHat/Cufflinks pipeline was performed, using the recently published draft genome sequence of CHO-K1 as reference. Additionally, the de novo contigs were mapped to the reference genome using GMAP and merged with the Cufflinks assembly using the cuffmerge software. With this approach 28,874 transcripts located on 16,492 gene loci could be assembled. Combining the results of both approaches, 65,561 transcripts were identified for CHO cell lines, which could be clustered by sequence identity into 17,598 gene clusters. PMID:24427317

Rupp, Oliver; Becker, Jennifer; Brinkrolf, Karina; Timmermann, Christina; Borth, Nicole; Pühler, Alfred; Noll, Thomas; Goesmann, Alexander

2014-01-01

116

Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability  

E-print Network

are constructed in two phases: (1) An initial DNA library is constructed on plastic microbeads by combinatorial of experiments of increasing size, currently the largest of which has 12 7 microbeads, each carrying

Reif, John H.

117

Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability  

E-print Network

are constructed in two phases: (1) An initial DNA library is constructed on plastic microbeads by combinatorial of experiments of increasing size, currently the largest of which has 127 microbeads, each carrying approximately

Reif, John H.

118

Harmonizing Databases? Using a Quasi-Experimental Design to Evaluate a Public Mental Health Re-entry Program1  

PubMed Central

Our study is the first-ever initiative to merge administrative databases in Massachusetts to evaluate an important public mental health program. It examines post-incarceration outcomes of adults with serious mental illness (SMI) enrolled in the Massachusetts Department of Mental Health (DMH) Forensic Transition Team (FTT) program. The program began in 1998 with the goal of transitioning offenders with SMI released from state and local correctional facilities utilizing a core set of transition activities. In this study we evaluate the program’s effectiveness using merged administrative data from various state agencies for the years 2007 – 2011, comparing FTT clients to released prisoners who, despite having serious mental health disorders, did not meet the criterion for DMH services. By systematically describing our original study design and the barriers we encountered, this report will inform future efforts to evaluate public programs using merged administrative databases and electronic health records. PMID:22436598

Deng, Xiaogang; Fisher, William; Fulwiler, Carl; Sambamoorthi, Usha; Johnson, Craig; Pinals, Debra A.; Sampson, Lisa; Siegfriedt, Julianne

2012-01-01

119

Errors in the interpretation of copy number variations due to the use of public databases as a reference.  

PubMed

The identification of new cryptic deletions and duplications can be used to improve prognostic classification in cancer. To obtain accurate results, it is necessary to discriminate between somatic alterations in the tumor cell and germline polymorphisms. For this purpose, copy number variation (CNV) public databases have been used as a reference. Nevertheless, the use of these databases may lead to erroneous results. Our main goal was to explore the limitations of the use of CNV databases, such as the Database of Genomic Variants (DGV), as the reference. To that end, we used pediatric acute lymphoblastic leukemia (ALL) as a model. We analyzed the genome-wide copy number profile of 23 ALL patients and conducted a comparison of the results obtained using the DGV with those obtained using the normal sample from the patient as the reference. Using only the DGV, 19% of alterations and 41% of polymorphisms were erroneously catalogued. Our results support the hypothesis that with the use of databases such as the DGV as the reference, a high percentage of the variations can be erroneously classified. PMID:24767712

Bastida-Lertxundi, Nerea; López-López, Elixabet; Piñán, M Angeles; Puiggros, Anna; Navajas, Aurora; Solé, Francesc; García-Orad, Africa

2014-04-01

120

Implications for DNA identification arising from an analysis of Australian forensic databases  

Microsoft Academic Search

Previous analyses of Australian samples have suggested that populations of the same broad racial group (Caucasian, Asian, Aboriginal) tend to be genetically similar across states. This suggests that a single national Australian database for each such group may be feasible, which would greatly facilitate casework. We have investigated samples drawn from each of these groups in different Australian states, and

Karen L. Ayres; Janet Chaseling; David J. Balding

2002-01-01

121

A Human Mitochondrial Genome Database  

NSDL National Science Digital Library

The Center for Molecular Medicine at Emory University maintains this human mitochondrial genome database, which offers information on Mitochondrial DNA Function Locations and Polypeptide Assignments as well as the relevant publication references. The database is initially searchable by gene, disease, and enzyme. Users can then refine their search by function, polymorphisms, or references (author, title, journal, year, or keyword). Users can also search the references directly via an Advanced Search. An additional resource at the site is a reference guide to mitomap tables featuring searchable (by keyword) information on specific mitochondrial DNA function locations and references. An opportunity to add publications to this database is available, if users find that pertinent papers have not been cited.

Brown, M. D.; Huoponen, K.; Katdare, G. C.; Kogelnik, A. M.; Lott, M. T.; Navathe, S. B.

1996-01-01

122

Development of Energy Consumption Database Management System of Existing Large Public Buildings  

E-print Network

The statistic data of energy consumption are the base of analyzing energy consumption. The scientific management method of energy consumption data and the development of database management system plays an important role in building energy...

Li, Y.; Zhang, J.; Sun, D.

2006-01-01

123

A PCR Multiplex and Database for Forensic DNA Identification of Dogs  

Microsoft Academic Search

ABSTRACT: Animal-derived trace evidence is a common,finding at crime scenes and may,provide an important link between,victim(s) and sus- pect(s). A database of 558 dogs of pure and mixed,breeds is described and analyzed,with two PCR multiplexes of 17 microsatellites. Summary statistics (number of alleles, expected and observed heterozygosity and power of exclusion) are compared between breeds. Marked population substructure in dog

Joy Halverson; Christopher Basten

2005-01-01

124

The Human Transcript Database: A Catalogue of Full Length cDNA Inserts  

SciTech Connect

The BCM Search Launcher provided improved access to web-based sequence analysis services during the granting period and beyond. The Search Launcher web site grouped analysis procedures by function and provided default parameters that provided reasonable search results for most applications. For instance, most queries were automatically masked for repeat sequences prior to sequence database searches to avoid spurious matches. In addition to the web-based access and arrangements that were made using the functions easier, the BCM Search Launcher provided unique value-added applications like the BEAUTY sequence database search tool that combined information about protein domains and sequence database search results to give an enhanced, more complete picture of the reliability and relative value of the information reported. This enhanced search tool made evaluating search results more straight-forward and consistent. Some of the favorite features of the web site are the sequence utilities and the batch client functionality that allows processing of multiple samples from the command line interface. One measure of the success of the BCM Search Launcher is the number of sites that have adopted the models first developed on the site. The graphic display on the BLAST search from the NCBI web site is one such outgrowth, as is the display of protein domain search results within BLAST search results, and the design of the Biology Workbench application. The logs of usage and comments from users confirm the great utility of this resource.

Bouckk John; Michael McLeod; Kim Worley; Richard Gibbs

1999-09-10

125

The MOSART Database: Linking the SART CORS Clinical Database to the Population-Based Massachusetts PELL Reproductive Public Health Data System.  

PubMed

Although Assisted Reproductive Technology (ART) births make up 1.6 % of births in the US, the impact of ART on subsequent infant and maternal health is not well understood. Clinical ART treatment records linked to population data would be a powerful tool to study long term outcomes among those treated or not by ART. This paper describes the development of a database intended to accomplish this task. We constructed the Massachusetts Outcomes Study of Assisted Reproductive Technology (MOSART) database by linking the Society of Assisted Reproductive Technologies Clinical Outcomes Reporting System (SART CORS) and the Massachusetts (MA) Pregnancy to Early Life Longitudinal (PELL) data systems for children born to MA resident women at MA hospitals between July 2004 and December 2008. PELL data representing 282,971 individual women and their 334,152 deliveries and 342,035 total births were linked with 48,578 cycles of ART treatment in SART CORS delivered to MA residents or women receiving treatment in MA clinics, representing 18,439 eligible women of whom 9,326 had 10,138 deliveries in this time period. A deterministic five phase linkage algorithm methodology was employed. Linkage results, accuracy, and concordance analyses were examined. We linked 9,092 (89.7 %) SART CORS outcome records to PELL delivery records overall, including 95.0 % among known MA residents treated in MA clinics; 70.8 % with full exact matches. There were minimal differences between matched and unmatched delivery records, except for unknown residency and out-of-state ART site. There was very low concordance of reported use of ART treatment between SART CORS and PELL (birth certificate) data. A total of 3.4 % of MA children (11,729) were identified from ART assisted pregnancies (6,556 singletons; 5,173 multiples). The MOSART linked database provides a strong basis for further longitudinal ART outcomes studies and supports the continued development of potentially powerful linked clinical-public health databases. PMID:24623195

Kotelchuck, Milton; Hoang, Lan; Stern, Judy E; Diop, Hafsatou; Belanoff, Candice; Declercq, Eugene

2014-11-01

126

A brief history of the formation of DNA databases in forensic science within Europe  

Microsoft Academic Search

The introduction of DNA analysis to forensic science brought with it a number of choices for analysis, not all of which were compatible. As laboratories throughout Europe were eager to use the new technology different systems became routine in different laboratories and consequently, there was no basis for the exchange of results. A period of co-operation then started in which

Peter D. Martin; Hermann Schmitter; Peter M. Schneider

2001-01-01

127

Mass spectrometric base composition profiling: Implications for forensic mtDNA databasing?  

PubMed Central

In forensic genetics mitochondrial DNA (mtDNA) is usually analyzed by direct Sanger-type sequencing (STS). This method is known to be laborious and sometimes prone to human error. Alternative methods have been proposed that lead to faster results. Among these are methods that involve mass-spectrometry resulting in base composition profiles that are, by definition, less informative than the full nucleotide sequence. Here, we applied a highly automated electrospray ionization mass spectrometry (ESI-MS) system (PLEX-ID) to an mtDNA population study to compare its performance with respect to throughput and concordance to STS. We found that the loss of information power was relatively low compared to the gain in speed and analytical standardization. The detection of point and length heteroplasmy turned out to be roughly comparable between the technologies with some individual differences related to the processes. We confirm that ESI-MS provides a valuable platform for analyzing mtDNA variation that can also be applied in the forensic context. PMID:24054029

Eduardoff, Mayra; Huber, Gabriela; Bayer, Birgit; Schmid, Dagmar; Anslinger, Katja; Gobel, Tanja; Zimmermann, Bettina; Schneider, Peter M.; Rock, Alexander W.; Parson, Walther

2013-01-01

128

Taxonomy, biodiversity and their publics in twenty-first-century DNA barcoding.  

PubMed

We examine the crafting of publics in the global Barcoding of Life Initiative (BOLI)--seen as crucial for re-invigorating, and democratizing, early-twenty-first-century taxonomic sciences and hence for actually achieving biodiversity protection. Our approach to the issue of publics differs from that of conventional public understanding of or engagement with science work. Combining science and technology studies with critical political theory allows us to examine the discursive and material formation of publics occurring within the science of DNA barcoding. Co-productionist theory suggests BOLI to be actively crafting its prospective publics imaginatively, as an integral part of its self-composition as public science. Drawing on the work of Laclau's On Populist Reason, we examine how such normatively weighted abstract publics are necessarily chronically incomplete, with an unavoidable tension between the universal and the particular. PMID:20977186

Ellis, Rebecca; Waterton, Claire; Wynne, Brian

2010-07-01

129

The low-template-DNA (stochastic) threshold--its determination relative to risk analysis for national DNA databases.  

PubMed

Although the low-template or stochastic threshold is in widespread use and is typically set to 150-200 rfu peak height, there has been no consideration on its determination and meaning. In this paper we propose a definition that is based upon the specific risk of wrongful designation of a heterozygous genotype as a homozygote which could lead to a false exclusion. Conversely, it is possible that a homozygote {a,a} could be designated as {a,F} where 'F' is a 'wild card', and this could lead to increased risk of false inclusion. To determine these risk levels, we analysed an experimental dataset that exhibited extreme drop-out using logistic regression. The derived probabilities are employed in a graphical model to determine the relative risks of wrongful designations that may cause false inclusions and exclusions. The methods described in this paper provide a preliminary solution of risk evaluation for any DNA process that employs a stochastic threshold. PMID:19215879

Gill, Peter; Puch-Solis, Roberto; Curran, James

2009-03-01

130

Discovery of Possible Gene Relationships through the Application of Self-Organizing Maps to DNA Microarray Databases  

PubMed Central

DNA microarrays and cell cycle synchronization experiments have made possible the study of the mechanisms of cell cycle regulation of Saccharomyces cerevisiae by simultaneously monitoring the expression levels of thousands of genes at specific time points. On the other hand, pattern recognition techniques can contribute to the analysis of such massive measurements, providing a model of gene expression level evolution through the cell cycle process. In this paper, we propose the use of one of such techniques –an unsupervised artificial neural network called a Self-Organizing Map (SOM)–which has been successfully applied to processes involving very noisy signals, classifying and organizing them, and assisting in the discovery of behavior patterns without requiring prior knowledge about the process under analysis. As a test bed for the use of SOMs in finding possible relationships among genes and their possible contribution in some biological processes, we selected 282 S. cerevisiae genes that have been shown through biological experiments to have an activity during the cell cycle. The expression level of these genes was analyzed in five of the most cited time series DNA microarray databases used in the study of the cell cycle of this organism. With the use of SOM, it was possible to find clusters of genes with similar behavior in the five databases along two cell cycles. This result suggested that some of these genes might be biologically related or might have a regulatory relationship, as was corroborated by comparing some of the clusters obtained with SOMs against a previously reported regulatory network that was generated using biological knowledge, such as protein-protein interactions, gene expression levels, metabolism dynamics, promoter binding, and modification, regulation and transport of proteins. The methodology described in this paper could be applied to the study of gene relationships of other biological processes in different organisms. PMID:24699245

Chavez-Alvarez, Rocio; Chavoya, Arturo; Mendez-Vazquez, Andres

2014-01-01

131

Interweaving Digital Narratives with Dynamic Archaeological Databases for the Public Presentation of Cultural Heritage  

Microsoft Academic Search

This paper describes a project that is currently being carried out in collaboration with the Interactive University of UC Berkeley in which a relational database comprising the contexts, materials, observations, and interpretations in visual, numerical and textual format from Neolithic excavations in Turkey (Çatalhöyük) and Yugoslavia (Opovo) provides the basic architecture for a series of hyperlinked \\

Ruth Tringham

132

Demographic and experiential correlates of public attitudes towards cell-free fetal DNA screening.  

PubMed

This study seeks to inform clinical application of cell-free fetal DNA (cffDNA) screening as a novel method for prenatal trisomy detection by investigating public attitudes towards this technology and demographic and experiential characteristics related to these attitudes. Two versions of a 25-item survey assessing interest in cffDNA and existing first-trimester combined screening for either trisomy 13 and 18 or trisomy 21 were distributed among 3,164 members of the United States public. Logistic regression was performed to determine variables predictive of interest in screening options. Approximately 47 % of respondents expressed an interest in cffDNA screening for trisomy 13, 18, and 21, with a majority interested in cffDNA screening as a stand-alone technique. A significantly greater percent would consider termination of pregnancy following a diagnosis of trisomy 13 or 18 (52 %) over one of trisomy 21 (44 %). Willingness to consider abortion of an affected pregnancy was the strongest correlate to interest in both cffDNA and first-trimester combined screening, although markedly more respondents expressed an interest in some form of screening (69 % and 71 %, respectively) than would consider termination. Greater educational attainment, higher income, and insurance coverage predicted interest in cffDNA screening; stronger religious identification also corresponded to decreased interest. Prior experience with disability and genetic testing was associated with increased interest in cffDNA screening. Several of these factors, in addition to advanced age and Asian race, were, in turn, predictive of respondents' increased willingness to consider post-diagnosis termination of pregnancy. In conclusion, divergent attitudes towards cffDNA screening-and prenatal options more generally - appear correlated with individual socioeconomic and religious backgrounds and experiences with disability and genetic testing. Clinical implementation and counseling for novel prenatal technologies should take these diverse stakeholder values into consideration. PMID:24715419

Sayres, Lauren C; Allyse, Megan; Goodspeed, Taylor A; Cho, Mildred K

2014-12-01

133

Identifying contributors of two-person DNA mixtures by familial database search.  

PubMed

The role of familial database search as a crime-solving tool has been increasingly recognized by forensic scientists. As an enhancement to the existing familial search approach on single source cases, this article presents our current progress in exploring the potential use of familial search to mixture cases. A novel method was established to predict the outcome of the search, from which a simple strategy for determining an appropriate scale of investigation by the police force is developed. Illustrated by an example using Swedish data, our approach is shown to have the potential for assisting the police force to decide on the scale of investigation, thereby achieving desirable crime-solving rate with reasonable cost. PMID:22270047

Chung, Yuk-Ka; Fung, Wing K

2013-01-01

134

DNA Identification of Mountain Lions Involved in Livestock Predation and Public Safety Incidents and Investigations  

Microsoft Academic Search

Using three case studies, we demonstrated the utility of techniques to analyze DNA from trace samples collected at sites of livestock predation and public safety incidents. Genetic analysis was used to determine species, individual identity, and relatedness between individuals. We documented the presence and individual identities of a mountain lion (Puma concolor) and a bobcat (Lynx rufus) from swab samples

H. B. Ernest; W. M. Boyce

135

Amplification volume reduction on DNA database samples using FTA™ Classic Cards.  

PubMed

The DNA forensic community always strives towards improvements in aspects such as sensitivity, robustness, and efficacy balanced with cost efficiency. Therefore our laboratory decided to study the feasibility of PCR amplification volume reduction using DNA entrapped in FTA™ Classic Card and to bring cost savings to the laboratory. There were a few concerns the laboratory needed to address. First, the kinetics of the amplification reaction could be significantly altered. Second, an increase in sensitivity might affect interpretation due to increased stochastic effects even though they were pristine samples. Third, statics might cause FTA punches to jump out of its allocated well into another thus causing sample-to-sample contamination. Fourth, the size of the punches might be too small for visual inspection. Last, there would be a limit to the extent of volume reduction due to evaporation and the possible need of re-injection of samples for capillary electrophoresis. The laboratory had successfully optimized a reduced amplification volume of 10 ?L for FTA samples. PMID:21543276

Wong, Hang Yee; Lim, Eng Seng Simon; Tan-Siew, Wai Fun

2012-03-01

136

Accelerated Publications The Affinity-Enhancing Roles of Flexible Linkers in Two-Domain DNA-Binding  

E-print Network

Accelerated Publications The Affinity-Enhancing Roles of Flexible Linkers in Two-Domain DNA made to design high-affinity DNA-binding proteins by linking two domains. Here a theory for guiding to enhance DNA-binding affinity over those of the individual domains (with dissociation constants KA and KB

Weston, Ken

137

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).  

PubMed

Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http://hive.biochemistry.gwu.edu/tools/biomuta/index.php; CSR: http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr; HIVE: http://hive.biochemistry.gwu.edu. PMID:24667251

Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J; Simonyan, Vahan; Mazumder, Raja

2014-01-01

138

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)  

PubMed Central

Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http://hive.biochemistry.gwu.edu/tools/biomuta/index.php; CSR: http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr; HIVE: http://hive.biochemistry.gwu.edu PMID:24667251

Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J.; Simonyan, Vahan; Mazumder, Raja

2014-01-01

139

DNA DNA DNA (d)DNA DNA DNA  

E-print Network

DNA DNA DNA DNA DNA DNA DNA DNA [ 2008] (d)DNA DNA DNA DNA 2 3 DNA DNA DNA DNA DNA DNA DNA (a) (c) (b) (d) #12;DNA DNA DNA DNA DNA DNA DNA DNA (b) DNA [Tanaka et al.2008] DNA DNA DNA DNA DNA DNA DNA #12;iGEM MIT MIT

Hagiya, Masami

140

BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species  

PubMed Central

Background MITE, TRIM and SINEs are miniature form transposable elements (mTEs) that are ubiquitous and dispersed throughout entire plant genomes. Tens of thousands of members cause insertion polymorphism at both the inter- and intra- species level. Therefore, mTEs are valuable targets and resources for development of markers that can be utilized for breeding, genetic diversity and genome evolution studies. Taking advantage of the completely sequenced genomes of Brassica rapa and B. oleracea, characterization of mTEs and building a curated database are prerequisite to extending their utilization for genomics and applied fields in Brassica crops. Findings We have developed BrassicaTED as a unique web portal containing detailed characterization information for mTEs of Brassica species. At present, BrassicaTED has datasets for 41 mTE families, including 5894 and 6026 members from 20 MITE families, 1393 and 1639 members from 5 TRIM families, 1270 and 2364 members from 16 SINE families in B. rapa and B. oleracea, respectively. BrassicaTED offers different sections to browse structural and positional characteristics for every mTE family. In addition, we have added data on 289 MITE insertion polymorphisms from a survey of seven Brassica relatives. Genes with internal mTE insertions are shown with detailed gene annotation and microarray-based comparative gene expression data in comparison with their paralogs in the triplicated B. rapa genome. This database also includes a novel tool, K BLAST (Karyotype BLAST), for clear visualization of the locations for each member in the B. rapa and B. oleracea pseudo-genome sequences. Conclusions BrassicaTED is a newly developed database of information regarding the characteristics and potential utility of mTEs including MITE, TRIM and SINEs in B. rapa and B. oleracea. The database will promote the development of desirable mTE-based markers, which can be utilized for genomics and breeding in Brassica species. BrassicaTED will be a valuable repository for scientists and breeders, promoting efficient research on Brassica species. BrassicaTED can be accessed at http://im-crop.snu.ac.kr/BrassicaTED/index.php. PMID:24948109

2014-01-01

141

Identification and quantification of glycerolipids in cotton fibers: reconciliation with metabolic pathway predictions from DNA databases.  

PubMed

The lipid profiles of cotton fiber cells were determined from total lipid extracts of elongating and maturing cotton fiber cells to see whether the membrane lipid composition changed during the phases of rapid cell elongation or secondary cell wall thickening. Total FA content was highest or increased during elongation and was lower or decreased thereafter, likely reflecting the assembly of the expanding cell membranes during elongation and the shift to membrane maintenance (and increase in secondary cell wall content) in maturing fibers. Analysis of lipid extracts by electrospray ionization and tandem MS (ESI-MS/MS) revealed that in elongating fiber cells (7-10 d post-anthesis), the polar lipids-PC, PE, PI, PA, phosphatidylglycerol, monogalactosyldiacylglycerol, digalactosyldiacylglycerol, and phosphatidylglycerol-were most abundant. These same glycerolipids were found in similar proportions in maturing fiber cells (21 dpa). Detailed molecular species profiles were determined by ESI-MS/MS for all glycerolipid classes, and ESI-MS/MS results were consistent with lipid profiles determined by HPLC and ELSD. The predominant molecular species of PC, PE, PI, and PA was 34:3 (16:0, 18:3), but 36:6 (18:3,18:3) also was prevalent. Total FA analysis of cotton lipids confirmed that indeed linolenic (18:3) and palmitic (16:0) acids were the most abundant FA in these cell types. Bioinformatics data were mined from cotton fiber expressed sequence tag databases in an attempt to reconcile expression of lipid metabolic enzymes with lipid metabolite data. Together, these data form a foundation for future studies of the functional contribution of lipid metabolism to the development of this unusual and economically important cell type. PMID:16296396

Wanjie, Sylvia W; Welti, Ruth; Moreau, Robert A; Chapman, Kent D

2005-08-01

142

INTEGRATING EARTH OBSERVATIONS DATA INTO GEOSPATIAL DATABASES THAT SUPPORT PUBLIC HEALTH DECISIONS  

Microsoft Academic Search

There are several reasons why public health communities do not use information from Earth observations routinely. Most notable among them are: (1) they need science results that verify, validate, and benchmark the statistical and economic benefits from these exotic inputs; and, (2) they lack the systems that would deliver such reliable information economically and swiftly in their already heavy workloads.

S. A. Morain; A. M. Budge

143

Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice --An et al. 133 (4): 2040 --PLANT PHYSIOLOGY Frame contained PDF file, click here to view  

E-print Network

Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice -- An et al. 133)9/20/2006 3:15:37 PM #12;Generation and Analysis of End Sequence Database for T-DNA Tagging Lines in Rice for T-DNA Tagging Lines in Rice1 Suyoung An2 , Sunhee Park2 , Dong-Hoon Jeong, Dong-Yeon Lee, Hong

Nei, Masatoshi

144

Sequence validation for the identification of the white-rot fungi bjerkandera in public sequence databases.  

PubMed

White-rot fungi of the genus Bjerkandera are cosmopolitan and have shown potential for industrial application and bioremediation. When distinguishing morphological characters are no longer present (e.g., cultures or dried specimen fragments), characterizing true sequences of Bjerkandera is crucial for accurate identification and application of the species. To build a framework for molecular identification of Bjerkandera, we carefully identified specimens of B. adusta and B. fumosa from Korea based on morphological characters, followed by sequencing the internal transcribed spacer region and 28S nuclear ribosomal large subunit. The phylogenetic analysis of Korean Bjerkandera specimens showed clear genetic differentiation between the two species. Using this phylogeny as a framework, we examined the identification accuracy of sequences available in GenBank. Analyses revealed that many Bjerkandera sequences in the database are either misidentified or unidentified. This study provides robust reference sequences for sequence-based identification of Bjerkandera, and further demonstrates the presence and dangers of incorrect sequences in GenBank. PMID:24912556

Jung, Paul Eunil; Fong, Jonathan J; Park, Myung Soo; Oh, Seung-Yoon; Kim, Changmu; Lim, Young Woon

2014-10-28

145

The Mission Accessible Near-Earth Object Survey Public Database Development Effort  

NASA Astrophysics Data System (ADS)

The Mission Accessible Near-Earth Object Survey (MANOS) began in August 2013 as a multi-year physical characterization survey that was awarded large survey status by NOAO. MANOS will target several hundred mission-accessible NEOs across visible and near-infrared wavelengths, ultimately providing a comprehensive catalog of physical properties (astrometry, light curves, spectra). The MANOS project will provide a resource that not only helps to manage our survey in a fully transparent, publicly accessible forum, but will also help to coordinate minor planet characterization efforts and target prioritization across multiple research groups. Working towards that goal, we are developing a portal for rapid, up to date, public dissemination of our data. Migrating the Lowell Astorb dataset to a SQL framework is a major step towards the modernization of the system and will make capable up-to-date deployment of data. This will further allow us to develop utilities of various complexity, such as a deltaV calculator, minor planet finder charts, and sophisticated ephemeri generation functions. We present the state of this effort and a preliminary timeline for functionality.

Burt, Brian; Moskovitz, Nicholas; Putnam, Lowell

2014-11-01

146

Microgravity Database  

NSDL National Science Digital Library

The European Space Agencies (ESA) Microgravity Database "gives scientists access to information regarding all experiments carried out on ESA and NASA missions by European scientists since the 1960s." Users choose from a physical or life sciences query form, then can search by experiment and investigators, mission and facility, publications and source, and more. Results provide the mission name, data, payload, research subject, publication information, an abstract, and any other available facts or related links. A very intuitive and well designed database, visitors should appreciate its unique and extensive content.

2000-01-01

147

Does language matter? A case study of epidemiological and public health journals, databases and professional education in French, German and Italian  

PubMed Central

Epidemiology and public health are usually context-specific. Journals published in different languages and countries play a role both as sources of data and as channels through which evidence is incorporated into local public health practice. Databases in these languages facilitate access to relevant journals, and professional education in these languages facilitates the growth of native expertise in epidemiology and public health. However, as English has become the lingua franca of scientific communication in the era of globalisation, many journals published in non-English languages face the difficult dilemma of either switching to English and competing internationally, or sticking to the native tongue and having a restricted circulation among a local readership. This paper discusses the historical development of epidemiology and the current scene of epidemiological and public health journals, databases and professional education in three Western European languages: French, German and Italian, and examines the dynamics and struggles they have today. PMID:18826570

Baussano, Iacopo; Brzoska, Patrick; Fedeli, Ugo; Larouche, Claudia; Razum, Oliver; Fung, Isaac C-H

2008-01-01

148

De-identifying a public use microdata file from the Canadian national discharge abstract database  

PubMed Central

Abstract Background The Canadian Institute for Health Information (CIHI) collects hospital discharge abstract data (DAD) from Canadian provinces and territories. There are many demands for the disclosure of this data for research and analysis to inform policy making. To expedite the disclosure of data for some of these purposes, the construction of a DAD public use microdata file (PUMF) was considered. Such purposes include: confirming some published results, providing broader feedback to CIHI to improve data quality, training students and fellows, providing an easily accessible data set for researchers to prepare for analyses on the full DAD data set, and serve as a large health data set for computer scientists and statisticians to evaluate analysis and data mining techniques. The objective of this study was to measure the probability of re-identification for records in a PUMF, and to de-identify a national DAD PUMF consisting of 10% of records. Methods Plausible attacks on a PUMF were evaluated. Based on these attacks, the 2008-2009 national DAD was de-identified. A new algorithm was developed to minimize the amount of suppression while maximizing the precision of the data. The acceptable threshold for the probability of correct re-identification of a record was set at between 0.04 and 0.05. Information loss was measured in terms of the extent of suppression and entropy. Results Two different PUMF files were produced, one with geographic information, and one with no geographic information but more clinical information. At a threshold of 0.05, the maximum proportion of records with the diagnosis code suppressed was 20%, but these suppressions represented only 8-9% of all values in the DAD. Our suppression algorithm has less information loss than a more traditional approach to suppression. Smaller regions, patients with longer stays, and age groups that are infrequently admitted to hospitals tend to be the ones with the highest rates of suppression. Conclusions The strategies we used to maximize data utility and minimize information loss can result in a PUMF that would be useful for the specific purposes noted earlier. However, to create a more detailed file with less information loss suitable for more complex health services research, the risk would need to be mitigated by requiring the data recipient to commit to a data sharing agreement. PMID:21861894

2011-01-01

149

Lung Image Databases-2  

Cancer.gov

Lung Image Database Consortium’s Normalized Relational Database • De-identified (anonymized) CT datasets • Publicly accessible • Web search tools • Cases from search results can be downloaded – ftp or DICOM De-identified CT datasets Digital Imaging and

150

Genome databases  

SciTech Connect

Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

Courteau, J.

1991-10-11

151

Comparative Study of Seven Commercial Kits for Human DNA Extraction from Urine Samples Suitable for DNA Biomarker-Based Public Health Studies  

PubMed Central

Human genomic DNA extracted from urine could be an interesting tool for large-scale public health studies involving characterization of genetic variations or DNA biomarkers as a result of the simple and noninvasive collection method. These studies, involving many samples, require a rapid, easy, and standardized extraction protocol. Moreover, for practicability, there is a necessity to collect urine at a moment different from the first void and to store it appropriately until analysis. The present study compared seven commercial kits to select the most appropriate urinary human DNA extraction procedure for epidemiological studies. DNA yield has been determined using different quantification methods: two classical, i.e., NanoDrop and PicoGreen, and two species-specific real-time quantitative (q)PCR assays, as DNA extracted from urine contains, besides human, microbial DNA also, which largely contributes to the total DNA yield. In addition, the kits giving a good yield were also tested for the presence of PCR inhibitors. Further comparisons were performed regarding the sampling time and the storage conditions. Finally, as a proof-of-concept, an important gene related to smoking has been genotyped using the developed tools. We could select one well-performing kit for the human DNA extraction from urine suitable for molecular diagnostic real-time qPCR-based assays targeting genetic variations, applicable to large-scale studies. In addition, successful genotyping was possible using DNA extracted from urine stored at ?20°C for several months, and an acceptable yield could also be obtained from urine collected at different moments during the day, which is particularly important for public health studies. PMID:25365790

Bali, Latifa El; Diman, Aurélie; Bernard, Alfred; Roosens, Nancy H. C.

2014-01-01

152

The Politics of Information: Building a Relational Database To Support Decision-Making at a Public University.  

ERIC Educational Resources Information Center

Describes creation of a relational database at the University of Washington supporting ongoing academic planning at several levels and affecting the culture of decision making. Addresses getting started; sharing the database; questions, worries, and issues; improving access to high-demand courses; the advising function; management of instructional…

Friedman, Debra; Hoffman, Phillip

2001-01-01

153

q -gram based database searching using a suffix array (QUASAR)  

Microsoft Academic Search

With the increasing amount of DNA sequence informationdeposited in public databases, searching for similarity to aquery sequence has become a basic operation in molecularbiology. But even today's fast algorithms reach theirlimits when applied to all-versus-all comparisons of largedatabases. Here we present a new database searching algorithmcalled QUASAR (Q-gram Alignment based on SuffixARrays) which was designed to quickly detect sequenceswith strong

Stefan Burkhardt; Andreas Crauser; Paolo Ferragina; Hans-Peter Lenhof; Eric Rivals; Martin Vingron

1999-01-01

154

Multiparameter Intelligent Monitoring in Intensive Care Ii (Mimic-Ii): A Public-Access Intensive Care Unit Database  

E-print Network

Objective: We sought to develop an intensive care unit research database applying automated techniques to aggregate high-resolution diagnostic and therapeutic data from a large, diverse population of adult intensive care ...

Saeed, Mohammed

155

BioModels Database  

NSDL National Science Digital Library

Hosted by the European Bioinformatics Institute, the BioModels Database is a collaborative, "new effort to develop a data resource that will allow biologist to store, search and retrieve published mathematical models of biological interests. The models in the BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc." The website allows visitors to browse and search the Database for models. The site also provides information about submitting models for the Database. It should be noted that submitted models must undergo tests conducted by BioModels Database curators before they are incorporated. [NL

156

Human Mitochondrial Protein Database  

NSDL National Science Digital Library

The Human Mitochondrial Protein Database (HMPDb) conveniently consolidates information from a number of other databases, including GenBank, Online Mendelian Inheritance in Man, and the Human Mitochondrial Genome Database. HMPDb "is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases" as well. Features include a general database search, a graphical tool for visualizing the mitochondrial DNA sequences, and 3D structures for mitochondrial proteins. Users are welcome to contact the National Institute of Standards and Technology with corrections or other information relating to the database.

157

Ku Binds Telomeric DNA in Vitro* (Received for publication, March 26, 1999, and in revised form, May 12, 1999)  

E-print Network

Ku Binds Telomeric DNA in Vitro* (Received for publication, March 26, 1999, and in revised form. Recently Ku has been shown to be a likely component of the telomeric complex in yeast, suggesting the possibility of a similar role for Ku at mammalian telomeres. However, long single- stranded G-rich overhangs

de Lange, Titia

158

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools.  

PubMed

The non-B DB, available at http://nonb.abcc.ncifcrf.gov, catalogs predicted non-B DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted repeats, mirror repeats, direct repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several genomes. Version 2.0 of the database revises and re-implements the motif discovery algorithms to better align with accepted definitions and thresholds for motifs, expands the non-B DNA-forming motifs coverage by including short tandem repeats and adds key visualization tools to compare motif locations relative to other genomic annotations. Non-B DB v2.0 extends the ability for comparative genomics by including re-annotation of the five organisms reported in non-B DB v1.0, human, chimpanzee, dog, macaque and mouse, and adds seven additional organisms: orangutan, rat, cow, pig, horse, platypus and Arabidopsis thaliana. Additionally, the non-B DB v2.0 provides an overall improved graphical user interface and faster query performance. PMID:23125372

Cer, Regina Z; Donohue, Duncan E; Mudunuri, Uma S; Temiz, Nuri A; Loss, Michael A; Starner, Nathan J; Halusa, Goran N; Volfovsky, Natalia; Yi, Ming; Luke, Brian T; Bacolla, Albino; Collins, Jack R; Stephens, Robert M

2013-01-01

159

A DNA Pairing-enhanced Conformation of Bacterial RecA Proteins* Received for publication, August 4, 2003, and in revised form, October 3, 2003  

E-print Network

A DNA Pairing-enhanced Conformation of Bacterial RecA Proteins* Received for publication, August 4A proteins of Escherichia coli (Ec) and Deino- coccus radiodurans (Dr) both promote a DNA strand exchange- stranded DNA-binding protein (SSB). In the absence of SSB, the initiation of strand exchange is greatly en

Cox, Michael M.

160

The DNA Binding Properties of Saccharomyces cerevisiae Rad51 (Received for publication, June 12, 1998, and in revised form, November 16, 1998)  

E-print Network

The DNA Binding Properties of Saccharomyces cerevisiae Rad51 Protein* (Received for publication Rad51 protein is the para- digm for eukaryotic ATP-dependent DNA strand ex- change proteins. To explain some of the unique charac- teristics of DNA strand exchange promoted by Rad51 protein, when

Kowalczykowski, Stephen C.

161

A New Model for Providing Cell-Free DNA and Risk Assessment for Chromosome Abnormalities in a Public Hospital Setting  

PubMed Central

Objective. Cell-free DNA (cfDNA) offers highly accurate noninvasive screening for Down syndrome. Incorporating it into routine care is complicated. We present our experience implementing a novel program for cfDNA screening, emphasizing patient education, genetic counseling, and resource management. Study Design. Beginning in January 2013, we initiated a new patient care model in which high-risk patients for aneuploidy received genetic counseling at 12 weeks of gestation. Patients were presented with four pathways for aneuploidy risk assessment and diagnosis: (1) cfDNA; (2) integrated screening; (3) direct-to-invasive testing (chorionic villus sampling or amniocentesis); or (4) no first trimester diagnostic testing/screening. Patients underwent follow-up genetic counseling and detailed ultrasound at 18–20 weeks to review first trimester testing and finalize decision for amniocentesis. Results. Counseling and second trimester detailed ultrasound were provided to 163 women. Most selected cfDNA screening (69%) over integrated screening (0.6%), direct-to-invasive testing (14.1%), or no screening (16.6%). Amniocentesis rates decreased following implementation of cfDNA screening (19.0% versus 13.0%, P < 0.05). Conclusion. When counseled about screening options, women often chose cfDNA over integrated screening. This program is a model for patient-directed, efficient delivery of a newly available high-level technology in a public health setting. Genetic counseling is an integral part of patient education and determination of plan of care. PMID:25101177

Wallerstein, Robert; Jelks, Andrea; Garabedian, Matthew J.

2014-01-01

162

DATARIs: Database on Research Institutes  

NSDL National Science Digital Library

The United Nations Institute for Disarmament Research (UNIDIR), in cooperation with the Stockholm International Peace Research Institute (SIPRI), maintain DATARIs, a collection of databases providing information from and about research institutes specializing in international relations and security. DATARIs includes directory databases on research institutes and documentation centers, bibliographic databases on research institute projects and publications, and a database providing information about databases maintained by associated research institutes. Each searchable database offers an easy-to-use search form interface, facilitating queries for users.

1998-01-01

163

Expanding the forensic German mitochondrial DNA control region database: genetic diversity as a function of sample size and microgeography.  

PubMed

Mitochondrial DNA control region sequences were determined in 109 unrelated German Caucasoid individuals from north west Germany for both hypervariable regions 1 (HV1) and 2 (HV2) and 100 polymorphic nucleotide positions (nps) were found, 63 in HV1 and 37 in HV2. A total of 100 different mtDNA lineages was revealed, of which 7 were shared by 2 individuals and 1 by 3 individuals. The probability of drawing a HV1 sequence match within the north west Germans or within published sets of south Germans and west Austrians is similar (within a factor of 2) to drawing a sequence match between any two of these three population samples. Furthermore, HV1 sequences of 700 male inhabitants of one village in Lower Saxony were generated and these showed a nearly linear increase of the number of different haplotypes with increasing number of individuals, demonstrating that the commonly used haplotype diversity measure (Nei 1987) for population samples tends to underestimate mtDNA diversity in the actual population. PMID:10460419

Pfeiffer, H; Brinkmann, B; Hühne, J; Rolf, B; Morris, A A; Steighner, R; Holland, M M; Forster, P

1999-01-01

164

Significant variance in genetic diversity among populations of Schistosoma haematobium detected using microsatellite DNA loci from a genome-wide database  

PubMed Central

Background Urogenital schistosomiasis caused by Schistosoma haematobium is widely distributed across Africa and is increasingly being targeted for control. Genome sequences and population genetic parameters can give insight into the potential for population- or species-level drug resistance. Microsatellite DNA loci are genetic markers in wide use by Schistosoma researchers, but there are few primers available for S. haematobium. Methods We sequenced 1,058,114 random DNA fragments from clonal cercariae collected from a snail infected with a single Schistosoma haematobium miracidium. We assembled and aligned the S. haematobium sequences to the genomes of S. mansoni and S. japonicum, identifying microsatellite DNA loci across all three species and designing primers to amplify the loci in S. haematobium. To validate our primers, we screened 32 randomly selected primer pairs with population samples of S. haematobium. Results We designed >13,790 primer pairs to amplify unique microsatellite loci in S. haematobium, (available at http://www.cebio.org/projetos/schistosoma-haematobium-genome). The three Schistosoma genomes contained similar overall frequencies of microsatellites, but the frequency and length distributions of specific motifs differed among species. We identified 15 primer pairs that amplified consistently and were easily scored. We genotyped these 15 loci in S. haematobium individuals from six locations: Zanzibar had the highest levels of diversity; Malawi, Mauritius, Nigeria, and Senegal were nearly as diverse; but the sample from South Africa was much less diverse. Conclusions About half of the primers in the database of Schistosoma haematobium microsatellite DNA loci should yield amplifiable and easily scored polymorphic markers, thus providing thousands of potential markers. Sequence conservation among S. haematobium, S. japonicum, and S. mansoni is relatively high, thus it should now be possible to identify markers that are universal among Schistosoma species (i.e., using DNA sequences conserved among species), as well as other markers that are specific to species or species-groups (i.e., using DNA sequences that differ among species). Full genome-sequencing of additional species and specimens of S. haematobium, S. japonicum, and S. mansoni is desirable to better characterize differences within and among these species, to develop additional genetic markers, and to examine genes as well as conserved non-coding elements associated with drug resistance. PMID:24499537

2013-01-01

165

Who owns what? Private ownership and the public interest in recombinant DNA technology in the 1970s.  

PubMed

This essay analyzes how academic institutions, government agencies, and the nascent biotech industry contested the legal ownership of recombinant DNA technology in the name of the public interest. It reconstructs the way a small but influential group of government officials and university research administrators introduced a new framework for the commercialization of academic research in the context of a national debate over scientific research's contributions to American economic prosperity and public health. They claimed that private ownership of inventions arising from public support would provide a powerful means to liberate biomedical discoveries for public benefit. This articulation of the causal link between private ownership and the public interest, it is argued, justified a new set of expectations about the use of research results arising from government or public support, in which commercialization became a new public obligation for academic researchers. By highlighting the broader economic and legal shifts that prompted the reconfiguration of the ownership of public knowledge in late twentieth-century American capitalism, the essay examines the threads of policy-informed legal ideas that came together to affirm private ownership of biomedical knowledge as germane to the public interest in the coming of age of biotechnology and genetic medicine. PMID:22073770

Yi, Doogab

2011-09-01

166

[Open access to academic scholarship as a public policy resource: a study of the Capes database on Brazilian theses and dissertations].  

PubMed

Access to scientific knowledge is a valuable resource than can inform and validate positions taken in formulating public policy. But access to this knowledge can be challenging, given the diversity and breadth of available scholarship. Communication between the fields of science and of politics requires the dissemination of scholarship and access to it. We conducted a study using an open-access search tool in order to map existent knowledge on a specific topic: agricultural contributions to the preservation of biodiversity. The present article offers a critical view of access to the information available through the Capes database on Brazilian theses and dissertations. PMID:21461460

da Silva Rosa, Teresa; Carneiro, Maria José

2010-12-01

167

Towards a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation.  

PubMed

In recent years there has been a dramatic increase in the number of freely accessible online databases serving the chemistry community. The internet provides chemistry data that can be used for data-mining, for computer models, and integration into systems to aid drug discovery. There is however a responsibility to ensure that the data are high quality to ensure that time is not wasted in erroneous searches, that models are underpinned by accurate data and that improved discoverability of online resources is not marred by incorrect data. In this article we provide an overview of some of the experiences of the authors using online chemical compound databases, critique the approaches taken to assemble data and we suggest approaches to deliver definitive reference data sources. PMID:22426180

Williams, Antony J; Ekins, Sean; Tkachenko, Valery

2012-07-01

168

76 FR 60031 - Notice of Order: Revisions to Enterprise Public Use Database Incorporating High-Cost Single...  

Federal Register 2010, 2011, 2012, 2013

...Incorporating High-Cost Single-Family Securitized Loan Data Fields and Technical Data Field Changes AGENCY: Federal Housing Finance Agency...Finance Agency (FHFA) shall make public certain data related to high-cost single-family loans...

2011-09-28

169

RecA Filament Dynamics during DNA Strand Exchange Reactions* (Received for publication, November 27, 1996)  

E-print Network

to rotation of the DNA substrates to drive branch movement unidirectionally. Here, we test key predictions a central prediction of the model. The RecA pro- tomer exchange is not required for, and does not occur is observed, and sig- nificant ATP is hydrolyzed, even though DNA strand exchange is entirely blocked

Cox, Michael M.

170

Ionic Liquids Database- (ILThermo)  

National Institute of Standards and Technology Data Gateway

SRD 147 Ionic Liquids Database- (ILThermo) (Web, free access)   IUPAC Ionic Liquids Database, ILThermo, is a free web research tool that allows users worldwide to access an up-to-date data collection from the publications on experimental investigations of thermodynamic, and transport properties of ionic liquids as well as binary and ternary mixtures containing ionic liquids.

171

Shakespeare Database Project  

NSDL National Science Digital Library

The Shakespeare database project at Westf=8Alische Wilhelms-Universitat Munster, Germany posts project news and information on publications its own WWW Home-Page. There is also a preview on the Shakespeare Database CD-ROM to be presented at the 1994 Frankfurt Bookfair.

172

GCOD - GeneChip Oncology Database  

PubMed Central

Background DNA microarrays have become a nearly ubiquitous tool for the study of human disease, and nowhere is this more true than in cancer. With hundreds of studies and thousands of expression profiles representing the majority of human cancers completed and in public databases, the challenge has been effectively accessing and using this wealth of data. Description To address this issue we have collected published human cancer gene expression datasets generated on the Affymetrix GeneChip platform, and carefully annotated those studies with a focus on providing accurate sample annotation. To facilitate comparison between datasets, we implemented a consistent data normalization and transformation protocol and then applied stringent quality control procedures to flag low-quality assays. Conclusion The resulting resource, the GeneChip Oncology Database, is available through a publicly accessible website that provides several query options and analytical tools through an intuitive interface. PMID:21291543

2011-01-01

173

Nanotechnology Database  

NSDL National Science Digital Library

Sponsored by the National Science Foundation and housed at the Loyola College in Maryland's International Technology Research Institute the Nanotechnology Database is a source of online information on major research centers, funding agencies, major reports, and books dealing with nanotechnology. The resources listed here are carefully selected and reviewed. The site is expected to grow with the continued support and updates from organizations and individuals in the field of nanotechnology. The list of resources is divided into the following categories: Academic, Industry, Government Laboratories, Government Agencies, Professional Societies, Non-Profit Organizations, Books, Periodicals, Reports, and Conferences. Each listing provides a brief summary (taken from that Website) and hyperlink to the resource (note: the book list links mostly take users to online booksellers). A submission form allows users to add a relevant organization or publication.

2001-01-01

174

Rainfall Simulation Database  

NSDL National Science Digital Library

The British Geomorphological Research Group maintains this rainfall simulation database site. The database includes information about rainfall simulators, as well as their set-up and use. Currently, the database is divided into laboratory, field, and dual-purpose (lab and field) rainfall simulators. For each simulator in the database, users will find information on: "Simulator identification; Contact information; Specification of simulator; performance of simulator; Table of intensities and rainfall characteristics; Costs; Summary of research conducted using the simulator; Publications; and Additional comments." A section on simulation calibration is planned, and a form is provided for those wishing to contribute simulators to the database. A lengthy selection of related references adds to the utility of the database.

175

Using data from the public project, Craig VenterSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: Craig Venter DNAi Location:Genome>the project>players>private project Using data from the public project Craig Venter, leader of the private effort at Celera Genomics, speaks about his company's reliance on the public data for reassembly of the Celera sequence.

2008-10-06

176

Buffmap Database  

NSDL National Science Digital Library

The Institut National de Recherche Agronomique (France) provides online databases of genomes for several organisms, including Buffalo. The database is updated as more data become available, and provide records on loci, genes, microsatellites, polymorphisms, probes, enzymes, homologue loci, alleles, primers, references, and links to external databases. Instructions for submitting data to the databases are provided on-site.

177

Analysis of Flanking Sequences from Dissociation Insertion Lines: A Database for Reverse Genetics in Arabidopsis  

Microsoft Academic Search

We have generated Dissociation ( Ds ) element insertions throughout the Arabidopsis genome as a means of random mutagenesis. Here, we present the molecular analysis of genomic sequences that flank the Ds insertions of 931 inde- pendent transposant lines. Flanking sequences from 511 lines proved to be identical or homologous to DNA or protein sequences in public databases, and disruptions

Serguei Parinov; Mayalagu Sevugan; Wei-Cai Yang; Mande Kumaran; Venkatesan Sundaresan

1999-01-01

178

Public concern over genetic manipulation, Alexander CapronSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Alexander Capron DNAi Location:Manipulation>Revolution>players>The controversy The Frankenstein factor Alexander Capron, a lawyer and specialist in bioethics, talks about how fear of Frankenstein captured the public fancy.

2008-10-06

179

Publicity.  

ERIC Educational Resources Information Center

Publicity for preschool cooperatives is described. Publicity helps produce financial support for preschool cooperatives. It may take the form of posters, brochures, newsletters, open house, newspaper coverage, and radio and television. Word of mouth and general good will in the community are the best avenues of publicity that a cooperative nursery…

Chisholm, Joan

180

DSSTOX STRUCTURE-SEARCHABLE PUBLIC TOXICITY DATABASE NETWORK: CURRENT PROGRESS AND NEW INITIATIVES TO IMPROVE CHEMO-BIOINFORMATICS CAPABILITIES  

EPA Science Inventory

The EPA DSSTox website (http://www/epa.gov/nheerl/dsstox) publishes standardized, structure-annotated toxicity databases, covering a broad range of toxicity disciplines. Each DSSTox database features documentation written in collaboration with the source authors and toxicity expe...

181

Title Journal/Database/Prepared For Author (s) Affiliation Website Publication Date Date of Survey/Study Topic/Summary Areas of Interest Offered Recommendations/Primary Action Steps Other Comments Some big issues include: Community, Environment, Housing,  

E-print Network

Title Journal/Database/Prepared For Author (s) Affiliation Website Publication Date Date of Survey Illinois University Marietta College https://www.apsanet.org/imgtest/hesli.pdf March-04 Spring 1997/ Fall 2003 Trying to increase the number of PhD candidates in Political science-- increase retention

182

Measuring Heterogeneity in Forensic Databases  

E-print Network

Measuring Heterogeneity in Forensic Databases Using Hierarchical Bayes Models: Computational Method in Forensic Databases Using Hierarchical Bayes Models''. It supplies details of the Markov Chain Monte Carlo technique employed. Some Key Words: DNA fingerprint, Gibbs Sampling, Markov Chain Monte Carlo. 1 #12; From

183

Biofuel Database  

National Institute of Standards and Technology Data Gateway

Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

184

The EMBL Nucleotide Sequence Database  

Microsoft Academic Search

The European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database (http:\\/\\/www.ebi.ac. uk\\/embl\\/index.html ) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank (USA). Data is exchanged amongst the collaborative databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups.

Wendy Baker; Alexandra Van Den Broek; Evelyn Camon; Pascal Hingamp; Peter Sterk; Guenter Stoesser; Mary Ann Tuli

2000-01-01

185

The EMBL nucleotide sequence database  

Microsoft Academic Search

The EMBL Nucleotide Sequence Database (http:\\/\\/ www.ebi.ac.uk\\/embl\\/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. Webin is

Guenter Stoesser; Wendy Baker; Alexandra Van Den Broek; Evelyn Camon; Maria Garcia-pastor; Carola Kanz; Tamara Kulikova; Vincent Lombard; Rodrigo Lopez; Helen E. Parkinson; Nicole Redaschi; Peter Sterk; Peter Stoehr; Mary Ann Tuli

2001-01-01

186

The Histone Database: an integrated resource for histones and histone fold-containing proteins  

PubMed Central

Eukaryotic chromatin is composed of DNA and protein components—core histones—that act to compactly pack the DNA into nucleosomes, the fundamental building blocks of chromatin. These nucleosomes are connected to adjacent nucleosomes by linker histones. Nucleosomes are highly dynamic and, through various core histone post-translational modifications and incorporation of diverse histone variants, can serve as epigenetic marks to control processes such as gene expression and recombination. The Histone Sequence Database is a curated collection of sequences and structures of histones and non-histone proteins containing histone folds, assembled from major public databases. Here, we report a substantial increase in the number of sequences and taxonomic coverage for histone and histone fold-containing proteins available in the database. Additionally, the database now contains an expanded dataset that includes archaeal histone sequences. The database also provides comprehensive multiple sequence alignments for each of the four core histones (H2A, H2B, H3 and H4), the linker histones (H1/H5) and the archaeal histones. The database also includes current information on solved histone fold-containing structures. The Histone Sequence Database is an inclusive resource for the analysis of chromatin structure and function focused on histones and histone fold-containing proteins. Database URL: The Histone Sequence Database is freely available and can be accessed at http://research.nhgri.nih.gov/histones/. PMID:22025671

Mariño-Ramírez, Leonardo; Levine, Kevin M.; Morales, Mario; Zhang, Suiyuan; Moreland, R. Travis; Baxevanis, Andreas D.; Landsman, David

2011-01-01

187

JAMSTEC Databases  

NSDL National Science Digital Library

From the Japan Marine Science and Technology Center (JAMSTEC) comes the JAMSTEC databases site. Visitors can access several databases and data sites including the Deep Seafloor Image Database, Japan ARGO Delayed-mode Database, the J-CAD Compact Arctic Drifter, MIRAI Data Web, Research Results Report System, Submarine Cable Data Center, and the TRITON Buoy Data Web site. All provide marine science related information from Japan and around the world.

2002-01-01

188

Database forensics  

Microsoft Academic Search

At the user or surface level, most Database Management System (DBMS) are similar. Most databases contain multiple tables, a standardized query language, primary key, foreign key, referential integrity, and metadata. With regard to physical file structures, concurrency mechanisms, security mechanisms, query optimization and datawarehouse techniques, databases may be radically different from each other. Most Forensic tools are too time consuming

Mario A. M. Guimaraes; Richard Austin; Huwida Said

2010-01-01

189

Database Administrator  

ERIC Educational Resources Information Center

The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

Moore, Pam

2010-01-01

190

Hippocratic Databases  

Microsoft Academic Search

The Hippocratic Oath has guided the conduct of physicians for centuries. Inspired by its tenet of preserving privacy, we argue that future database systems must include responsibility for the pri- vacy of data they manage as a founding tenet. We enunciate the key privacy principles for such Hip- pocratic database systems. We propose a straw- man design for Hippocratic databases,

Rakesh Agrawal; Jerry Kiernan; Ramakrishnan Srikant; Yirong Xu

2002-01-01

191

Hydrocarbon Impacts Database  

NSDL National Science Digital Library

The Hydrocarbon Impacts (HI) database is a subset of the University of Calgary's Arctic Institute of North America's Arctic Science and Technology Information System database. More than 5,100 records describe "publications and research projects about the environmental impacts, socio-economic effects and regulation of hydrocarbon exploration, development and transportation in northern Canada." Users can search by record type, keyword, subject code, geographic code, author, and year, as well as an advanced search feature to locate the information. Well designed and easy to use, the database provides those interested in this narrow subject field a helpful resource.

192

Method and system for normalizing biometric variations to authenticate users from a public database and that ensures individual biometric data privacy  

DOEpatents

A password system comprises a set of codewords spaced apart from one another by a Hamming distance (HD) that exceeds twice the variability that can be projected for a series of biometric measurements for a particular individual and that is less than the HD that can be encountered between two individuals. To enroll an individual, a biometric measurement is taken and exclusive-ORed with a random codeword to produce a "reference value." To verify the individual later, a biometric measurement is taken and exclusive-ORed with the reference value to reproduce the original random codeword or its approximation. If the reproduced value is not a codeword, the nearest codeword to it is found, and the bits that were corrected to produce the codeword to it is found, and the bits that were corrected to produce the codeword are also toggled in the biometric measurement taken and the codeword generated during enrollment. The correction scheme can be implemented by any conventional error correction code such as Reed-Muller code R(m,n). In the implementation using a hand geometry device an R(2,5) code has been used in this invention. Such codeword and biometric measurement can then be used to see if the individual is an authorized user. Conventional Diffie-Hellman public key encryption schemes and hashing procedures can then be used to secure the communications lines carrying the biometric information and to secure the database of authorized users.

Strait, Robert S. (Oakland, CA); Pearson, Peter K. (Livermore, CA); Sengupta, Sailes K. (Livermore, CA)

2000-01-01

193

Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software  

PubMed Central

Metabolism has been identified as a defining factor in drug development success or failure because of its impact on many aspects of drug pharmacology, including bioavailability, half-life and toxicity. In this article, we provide an outline and descriptions of the resources for metabolism-related property predictions that are currently either freely or commercially available to the public. These resources include databases with data on, and software for prediction of, several end points: metabolite formation, sites of metabolic transformation, binding to metabolizing enzymes and metabolic stability. We attempt to place each tool in historical context and describe, wherever possible, the data it was based on. For predictions of interactions with metabolizing enzymes, we show a typical set of results for a small test set of compounds. Our aim is to give a clear overview of the areas and aspects of metabolism prediction in which the currently available resources are useful and accurate, and the areas in which they are inadequate or missing entirely. PMID:23088273

Peach, Megan L; Zakharov, Alexey V; Liu, Ruifeng; Pugliese, Angelo; Tawa, Gregory; Wallqvist, Anders; Nicklaus, Marc C

2014-01-01

194

The Hawaiian Algal Database: a laboratory LIMS and online resource for biodiversity data  

PubMed Central

Background Organization and presentation of biodiversity data is greatly facilitated by databases that are specially designed to allow easy data entry and organized data display. Such databases also have the capacity to serve as Laboratory Information Management Systems (LIMS). The Hawaiian Algal Database was designed to showcase specimens collected from the Hawaiian Archipelago, enabling users around the world to compare their specimens with our photographs and DNA sequence data, and to provide lab personnel with an organizational tool for storing various biodiversity data types. Description We describe the Hawaiian Algal Database, a comprehensive and searchable database containing photographs and micrographs, geo-referenced collecting information, taxonomic checklists and standardized DNA sequence data. All data for individual samples are linked through unique accession numbers. Users can search online for sample information by accession number, numerous levels of taxonomy, or collection site. At the present time the database contains data representing over 2,000 samples of marine, freshwater and terrestrial algae from the Hawaiian Archipelago. These samples are primarily red algae, although other taxa are being added. Conclusion The Hawaiian Algal Database is a digital repository for Hawaiian algal samples and acts as a LIMS for the laboratory. Users can make use of the online search tool to view and download specimen photographs and micrographs, DNA sequences and relevant habitat data, including georeferenced collecting locations. It is publicly available at . PMID:19728892

Wang, Norman; Sherwood, Alison R; Kurihara, Akira; Conklin, Kimberly Y; Sauvage, Thomas; Presting, Gernot G

2009-01-01

195

DATABASE AUTHENTICATION BY DISTORTION FREE WATERMARKING  

E-print Network

DATABASE AUTHENTICATION BY DISTORTION FREE WATERMARKING Sukriti Bhattacharya and Agostino Cortesi@dsi.unive.it, cortesi@unive.it Keywords: Database watermarking, ZAW, Public key watermark, Abstract interpretation the verification of integrity of the relational databases by using a public zero distortion authentication

Cortesi, Tino

196

Publications  

NSDL National Science Digital Library

This is an article from The Physiologist. "If you have published an article in one of the APS research journals in the second half of 2007, you may have noticed that the time it took from acceptance of your manuscript to final publication was much shorter than in the past. That is because the Publications Department decreased that time from an average of four months to two and a half months."

2008-02-01

197

IOPI Database of Plant Databases  

NSDL National Science Digital Library

The International Organization for Plant Information (IOPI), a Commission of the International Union of Biological Sciences (IUBS), manages the Database of Plant Databases (DPD). The DPD is a global list of plant databases including Taxonomic databases ("with systematic information on families or genera, or for Flora projects"); Collection catalogs (usually of herbaria); and DELTA datasets (DELTA is "the Description Language for Taxonomy, a data format for character data, used for identification, key construction and the generation of descriptions."). The DPD may be searched using numerous specified fields, or it may be viewed in its entirety -- by Database Name, Host Name, or Host Country. Though bare bones in appearance, this extensive database contains a gold mine of information, with hundreds of hyperlinks to valuable plant databases.

198

Fast decision tree-based method to index large DNA-protein sequence databases using hybrid distributed-shared memory programming model.  

PubMed

In recent times, the size of biological databases has increased significantly, with the continuous growth in the number of users and rate of queries; such that some databases have reached the terabyte size. There is therefore, the increasing need to access databases at the fastest rates possible. In this paper, the decision tree indexing model (PDTIM) was parallelised, using a hybrid of distributed and shared memory on resident database; with horizontal and vertical growth through Message Passing Interface (MPI) and POSIX Thread (PThread), to accelerate the index building time. The PDTIM was implemented using 1, 2, 4 and 5 processors on 1, 2, 3 and 4 threads respectively. The results show that the hybrid technique improved the speedup, compared to a sequential version. It could be concluded from results that the proposed PDTIM is appropriate for large data sets, in terms of index building time. PMID:24794073

Jaber, Khalid Mohammad; Abdullah, Rosni; Rashid, Nur'Aini Abdul

2014-01-01

199

A database of expressed genes from Cochliomyia hominivorax (Diptera: Calliphoridae).  

PubMed

We used an expressed sequence tag and 454 pyrosequencing approach to initiate a study of the genome of the screwworm, Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae). Two normalized cDNA libraries were constructed from RNA isolated from embryos and second instar larvae from the Panama 95 strain. Approximately 5,400 clones from each library were sequenced from both the 5' and 3' directions using the Sanger method. In addition, double-stranded cDNA was prepared from random-primed polyA RNA purified from embryos, second-instar larvae, adult males, and adult females. These four cDNA samples were used for 454 pyrosequencing that produced approximately 300,000 independent sequences. Sequences were assembled into a database of assembled contigs and singletons and used to search public protein databases and annotate the sequences. The full database consists of 6,076 contigs and 58,221 singletons assembled from both the traditional expressed sequence tag (EST) and 454 sequences. Annotation of the data led to the identification of several gene coding regions with possible roles in sex determination in the screwworm. This database will facilitate the design of microarray and other experiments to study screwworm gene expression on a larger scale than previously possible. PMID:19769042

Guerrero, F D; Dowd, S E; Djikeng, A; Wiley, G; Macmil, S; Saldivar, L; Najar, F; Roe, B A

2009-09-01

200

Computer Note A Prototype Object Database for  

E-print Network

Computer Note A Prototype Object Database for Mitochondrial DNA Variation J. E. NEIGEL AND P preserved. We hope to prevent further loss by establishing a community database for population genetic surveys. We explored the feasibility of a population genetics database by developing a prototype

Neigel, Joseph E.

201

ii The query may not be an exact match or even partial match with any data in the database, but since DNA annealing a nity methods work  

E-print Network

will be made by adapting error- resilient and optimum rate techniques, which originate in computational of the social security number of the person whose DNA was sampled, cell type, the date, further medical data disciplines. A Motivating Example: Massively Parallel I O using DNA Chips. For exam- ple, let us consider

Reif, John H.

202

Investigating Evolutionary Questions Using Online Molecular Databases.  

ERIC Educational Resources Information Center

Recommends using online molecular databases as teaching tools to illustrate evolutionary questions and concepts while introducing students to public molecular databases. Provides activities in which students make molecular comparisons between species. (YDS)

Puterbaugh, Mary N.; Burleigh, J. Gordon

2001-01-01

203

Annual Review of Database Development: 1992.  

ERIC Educational Resources Information Center

Reviews recent trends in databases and online systems. Topics discussed include new access points for established databases; acquisitions, consolidations, and competition between vendors; European coverage; international services; online reference materials, including telephone directories; political and legal materials and public records;…

Basch, Reva

1992-01-01

204

Neogene Mammal Database  

NSDL National Science Digital Library

There are plenty of mammal databases that deal with existing taxonomies and such, but where can one go to find information about land mammal taxa from the Eurasian Miocene to Pleistocene periods? They need look no further than this fine website, which provides access to such material, courtesy of an international advisory board, headed by Mikael Fortelius of the University of Helsinki. First-time visitors may want to look over the data conventions section first. Here they can learn about the proper use of taxonomic fields, and also view such taxonomic examples from the database. Users may also want to look over the browsing section, as it serves as a good orientation to effectively using the database. For those engaged in scholarly endeavors related to the field, there is also a publications section that offers access to recent works that draw on this rather voluminous database.

205

Database Manager  

ERIC Educational Resources Information Center

It is normal practice today for organizations to store large quantities of records of related information as computer-based files or databases. Purposeful information is retrieved by performing queries on the data sets. The purpose of DATABASE MANAGER is to communicate to students the method by which the computer performs these queries. This…

Martin, Andrew

2010-01-01

206

Federal databases  

Microsoft Academic Search

Accident statistics on all modes of transportation are available as risk assessment analytical tools through several federal agencies. This paper reports on the examination of the accident databases by personal contact with the federal staff responsible for administration of the database programs. This activity, sponsored by the Department of Energy through Sandia National Laboratories, is an overview of the national

M. J. Welch; B. W. Welles

1988-01-01

207

The EMBL Nucleotide Sequence Database  

Microsoft Academic Search

The EMBL Nucleotide Sequence Database (http:\\/\\/ www.ebi.ac.uk\\/embl\\/), maintained at the European Bioinformatics Institute (EBI), incorporates, organ- izes and distributes nucleotide sequences from public sources. The database is a part of an inter- national collaboration with DDBJ (Japan) and GenBank (USA). Data are exchanged between the collaborating databases on a daily basis to achieve optimal synchrony. The web-based tool, Webin, is

Tamara Kulikova; Philippe Aldebert; Nicola Althorpe; Wendy Baker; Kirsty Bates; Paul Browne; Alexandra Van Den Broek; Guy Cochrane; Karyn Duggan; Ruth Eberhardt; Nadeem Faruque; Maria Garcia-pastor; Nicola Harte; Carola Kanz; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Michelle Mchale; Francesco Nardone; Ville Silventoinen; Peter Stoehr; Guenter Stoesser; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler

2004-01-01

208

The National Ag Safety Database  

NSDL National Science Digital Library

The University of Florida originally made this directory, a subset of its National Agricultural Safety Database CD-ROM, available on the web. Since then the database has undergone several updates. The Directory "contains contact information on safety professionals and organizations throughout the US," and "health and safety publications from 32 states, 4 federal agencies and 5 national organizations" and can be browsed or searched. The creators of the database have gone to great lengths to improve this site over the years.

1995-01-01

209

NSFC Databases  

NSDL National Science Digital Library

The National Environmental Services Center (NESC) is based at West Virginia University and "serves as a clearinghouse for information about drinking water, wastewater, environmental training, and solid waste management in communities serving fewer than 10,000 individuals." As part of the NSFC larger Web site, the Databases page offers three online databases that can be accessed free after an initial registration. The Regulations Database contains copies of regulations for onsite wastewater treatment systems in 48 states, the Bibliographic Database stores thousands of articles dealing with onsite and small community wastewater issues, and the Manufacturers and Consultants Database houses a list of industry contacts for wastewater products and consulting services. Much more is available within the larger NSFC site and readers are encouraged to take a look through its contents.

2001-01-01

210

Laboratory information management systems for DNA barcoding.  

PubMed

In the field of molecular biology, laboratory information management systems (LIMSs) have been created to track workflows through a process pipeline. For the purposes of DNA barcoding, this workflow involves tracking tissues through extraction, PCR, cycle sequencing, and consensus assembly. Importantly, a LIMS that serves the DNA barcoding community must link required elements for public submissions (e.g., primers, trace files) that are generated in the molecular lab with specimen metadata. Here, we demonstrate an example workflow of a specimen's entry into the LIMS database to the publishing of the specimen's genetic data to a public database using Geneious bioinformatics software. Throughout the process, the connections between steps in the workflow are maintained to facilitate post-processing annotation, structured reporting, and fully transparent edits to reduce subjectivity and increase repeatability. PMID:22684961

Parker, Meaghan; Stones-Havas, Steven; Starger, Craig; Meyer, Christopher

2012-01-01

211

GlycomeDB - integration of open-access carbohydrate structure databases  

PubMed Central

Background Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases. Results We have implemented procedures which download the structures contained in the seven major databases, e.g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). We have created a new database called GlycomeDB, containing all structures, their taxonomic annotations and references (IDs) for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators. Conclusion GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource. PMID:18803830

Ranzinger, Rene; Herget, Stephan; Wetter, Thomas; von der Lieth, Claus-Wilhelm

2008-01-01

212

Fun Databases: My Top Ten.  

ERIC Educational Resources Information Center

Provides reviews of 10 online databases: Consumer Reports; Public Opinion Online; Encyclopedia of Associations; Official Airline Guide Adventure Atlas and Events Calendar; CENDATA; Hollywood Hotline; Fearless Taster; Soap Opera Summaries; and Human Sexuality. (LRW)

O'Leary, Mick

1992-01-01

213

Spatial Database Systems Tutorial Notes  

E-print Network

with extent city river cable highway forest lake city #12;Ralf Hartmut Güting, Tutorial Spatial Database ownership · "environments" of points Voronoi diagram · highways, streets · railways, public transport

Güting, Ralf Hartmut

214

DFCI Gene Index Project: Genomic Databases for Plants, Animals, Protist, and Fungi from the Dana-Farber Cancer Institute  

DOE Data Explorer

The DFCI Gene Index Project creates databases for specific organisms. The goal for these databases is to provide an analysis of publicly available Expressed Sequence Transcripts (ESTs). ESTs are fragments of genes that were, at some time, copied from DNA to RNA. and gene sequence data to identify transcrips. The databases are in zipped files and free for download. The website also provides software and tools for use with the data, along with instructions from the website on how to link to background resources. The Gene Indices are organized into four categories: Animals, Plants, Protist, and Fungi.

215

BIOMARKERS DATABASE  

EPA Science Inventory

This database was developed by assembling and evaluating the literature relevant to human biomarkers. It catalogues and evaluates the usefulness of biomarkers of exposure, susceptibility and effect which may be relevant for a longitudinal cohort study. In addition to describing ...

216

Application of Biomolecular Computing to Medical Science: A Biomolecular Database System for Storage, Processing & Retrieval of Genetic Information & Material  

E-print Network

how these queries can be executed by applying recombinant DNA operations on this Biomolecular Database recombinant DNA operations. We also utilize recent biotechnology developments (recombinant DNA technology, DNA & Retrieval of Genetic Information & Material. The recent advances in biotechnology (recombinant DNA

Reif, John H.

217

Addition of a breeding database in the Genome Database for Rosaceae  

PubMed Central

Breeding programs produce large datasets that require efficient management systems to keep track of performance, pedigree, geographical and image-based data. With the development of DNA-based screening technologies, more breeding programs perform genotyping in addition to phenotyping for performance evaluation. The integration of breeding data with other genomic and genetic data is instrumental for the refinement of marker-assisted breeding tools, enhances genetic understanding of important crop traits and maximizes access and utility by crop breeders and allied scientists. Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington State University apple breeding program and subsequently expanded to fit datasets from other Rosaceae breeders. The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data. Breeders can search accessions within the GDR to identify individuals with specific trait combinations. Results from Search by Parentage lists individuals with parents in common and results from Individual Variety pages link to all data available on each chosen individual including pedigree, phenotypic and genotypic information. Genotypic data are searchable by markers and alleles; results are linked to other pages in the GDR to enable the user to access tools such as GBrowse and CMap. This breeding database provides users with the opportunity to search datasets in a fully targeted manner and retrieve and compare performance data from multiple selections, years and sites, and to output the data needed for variety release publications and patent applications. The breeding database facilitates efficient program management. Storing publicly available breeding data in a database together with genomic and genetic data will further accelerate the cross-utilization of diverse data types by researchers from various disciplines. Database URL: http://www.rosaceae.org/breeders_toolbox PMID:24247530

Evans, Kate; Jung, Sook; Lee, Taein; Brutcher, Lisa; Cho, Ilhyung; Peace, Cameron; Main, Dorrie

2013-01-01

218

Quakeline Database  

NSDL National Science Digital Library

With information on more than 33,000 records, Quakeline is a bibliographic database for materials on earthquakes, earthquake engineering, and natural hazard mitigation. Hosted by the Multidisciplinary Center for Earthquake Engineering Research (MCEER) Information Service, the database houses records for journal articles, conference papers, technical reports, maps, and videotapes. The MCEER Information Service actually possesses all of the documents cited in Quakeline. Instructions for ordering documents are included at the site.

219

Multimedia Databases  

Microsoft Academic Search

.  The rapidly growing interest in building multimedia tools and applications has created a need for the development of multimedia\\u000a database management systems (MMDBMSs) as a tool for efficient organization, storage and retrieval of multimedia objects. We\\u000a begin with a word about traditional database management systems (DBMSs). Then we present an overview of the MMDBMS research\\u000a issues, challenges, methods, models, and

Arcot Desai Narasimhalu

1996-01-01

220

Content based information retrieval in forensic image databases.  

PubMed

This paper gives an overview of the various available image databases and ways of searching these databases on image contents. The developments in research groups of searching in image databases is evaluated and compared with the forensic databases that exist. Forensic image databases of fingerprints, faces, shoeprints, handwriting, cartridge cases, drugs tablets, and tool marks are described. The developments in these fields appear to be valuable for forensic databases, especially that of the framework in MPEG-7, where the searching in image databases is standardized. In the future, the combination of the databases (also DNA-databases) and possibilities to combine these can result in stronger forensic evidence. PMID:11908596

Geradts, Zeno; Bijhold, Jurrien

2002-03-01

221

Identification of RNA editing sites in the SNP database  

PubMed Central

The relationship between human inherited genomic variations and phenotypic differences has been the focus of much research effort in recent years. These studies benefit from millions of single-nucleotide polymorphism (SNP) records available in public databases, such as dbSNP. The importance of identifying false dbSNP records increases with the growing role played by SNPs in linkage analysis for disease traits. In particular, the emerging understanding of the abundance of DNA and RNA editing calls for a careful distinction between inherited SNPs and somatic DNA and RNA modifications. In order to demonstrate that some of the SNP database records are actually somatic modification, we focus on one type of these modifications, namely A-to-I RNA editing, and present evidence for hundreds of dbSNP records that are actually editing sites. We provide a list of 102 RNA editing sites previously annotated in dbSNP database as SNPs, and experimentally validate seven of these. Interestingly, we show how dbSNP can serve as a starting point to look for new editing sites. Our results, for this particular type of RNA editing, demonstrate the need for a careful analysis of SNP databases in light of the increasing recognition of the significance of somatic sequence modifications. PMID:16100382

Eisenberg, Eli; Adamsky, Konstantin; Cohen, Lital; Amariglio, Ninette; Hirshberg, Abraham; Rechavi, Gideon; Levanon, Erez Y.

2005-01-01

222

Hospital Records Database  

NSDL National Science Digital Library

This new joint project from the Wellcome Trust and the UK Public Record Office helps researchers locate records of hospitals all over the UK. The database currently contains over 2,800 entries and may be searched by hospital or town name. Information contained in the database includes administrative details of the hospitals, location and covering dates of administrative and clinical records, and the existence of lists, catalogs or other finding aids. A sample search for "royal" under hospital name returned 210 records, and one for "Manchester" under town name produced 124 returns. While the target audience of this database -- researchers in British medical history -- is rather specialized, this new resource will prove extremely useful for these scholars and their students.

223

Alcohol Industry & Policy Database  

NSDL National Science Digital Library

The Marin Institute for the Prevention of Alcohol and Other Drug Problems maintains the Alcohol Industry & Policy Database, which contains bibliographic citations and abstracts for more than 13,000 articles and news stories on the alcohol beverage industry, alcohol policy, and the prevention of alcohol-related problems. The citations in the database span from 1991 to the present and are updated monthly. Users may conduct cross-field queries of the database by keywords, subject headings, company name, and publication date. The search facility includes Word Wheels, which are interactive Java applets that help users to identify indexed terms quickly, thereby "eliminat[ing] trial-and-error searching [and] produc[ing] more accurate searches."

Problems., Marin I.

224

Solubility Database  

National Institute of Standards and Technology Data Gateway

SRD 106 IUPAC-NIST Solubility Database (Web, free access)   These solubilities are compiled from 18 volumes (Click here for List) of the International Union for Pure and Applied Chemistry(IUPAC)-NIST Solubility Data Series. The database includes liquid-liquid, solid-liquid, and gas-liquid systems. Typical solvents and solutes include water, seawater, heavy water, inorganic compounds, and a variety of organic compounds such as hydrocarbons, halogenated hydrocarbons, alcohols, acids, esters and nitrogen compounds. There are over 67,500 solubility measurements and over 1800 references.

225

Progress towards a Spacecraft-Associated Microbial Meta-database (SAMM)  

NASA Astrophysics Data System (ADS)

The microbial inventories within the assembly facilities for spacecraft represent the primary pool of forward contaminants that may compromise life-detection missions. Accordingly, we are constructing a meta-database of these microorganisms for the purpose of building a bioinformatic resource for planetary protection and astrobiology-related endeavors. Using student-led efforts, the meta-database is being constructed from literature reports and is inclusive of both isolated microorganisms and those solely detected through DNA-based techniques. The Spacecraft-Associated Microbial Meta-database (SAMM) currently includes over 800 entries that are organized using 32 meta-tags involving taxonomy, location of isolation (facility and component), category of characterization (culture and/or genetic), types of characterizations (e.g., culture, 16s rDNA, phylochip, FAME, and DNA hybridization), growth conditions, Gram stain, and general physiological traits (e.g., sporulation, extremotolerance, and respiration properties). Interrogations on the database show that the cleanrooms at Kennedy Space Center (KSC) are ~ 2-fold greater in diversity in bacterial genera when compared to the Jet Propulsion Laboratory (JPL), and that bacteria related to water, plant, and human environments are more often associated with the KSC-specific genera. These results are parallel to those reported in the literature, and hence serve as benchmarks demonstrating the bioinformatic potential of this meta-database. The ultimate plans for SAMM include public availability, expansion through crowdsourcing efforts, and potential use as a companion resource to the culture collections assembled by DSMZ and JPL.

Mogul, Rakesh; Keagy, Laura; Nava, Argelia; Zerehi, Farah

226

Environmental databases  

SciTech Connect

Knowledge of environmental phenomena, their anticipation, understanding, and prognosis, has increased tremendously with simultaneous advances in computer technology. Industrial growth, now seen to impact the environment deleteriously, is permitted only after assessing its impact on the environment through the use of computing technology or modeling. Environmental management is perhaps the only field where man attempts to write the book of rules without any or with little experience. Though compliance and remediation are the current focus of environmental agencies, the stress is now on pollution prevention. Today, computers are huge repositories of information enabling quick access and application in unprecedented environmental episodes or emergencies, and providing sophisticated help in planning and decision making, to avert any catastrophe. Databases play a crucial role in this process. Prediction and/or planning studies, the accuracy of results, possibilities of solution existence, identification of problem areas, documentation of the solutions, report generation, and most of the situations arising typically in air dispersion can be conveniently handled with and due to databases. This review briefly describes popular databases available, their use, and the contact address, to acquire them. The review mainly focuses on those databases available in the air area.

Kumar, A.; Riswadkar, R. (Univ. of Toledo, OH (United States))

1992-05-01

227

The Molecular Biology Database Collection: 2005 update  

PubMed Central

The Nucleic Acids Research Molecular Biology Database Collection is a public online resource that lists the databases described in this and previous issues of Nucleic Acids Research together with other databases of value to the biologist and available throughout the world. All databases included in this Collection are freely available to the public. The 2005 update includes 719 databases, 171 more than the 2004 one. The databases are organized in a hierarchical classification that simplifies the process of finding the right database for any given task. The growing number of databases related to immunology, plant and organelle research have been accommodated by separating them into three new categories. The database summaries provide brief descriptions of the databases, contact details, appropriate references and acknowledgements. The online summaries also serve as a venue for the maintainers of each database to introduce database updates and other improvements in the scope and tools. These updates are particularly important for those databases that have not been described in print in the recent past. The database list and summaries are available online at the Nucleic Acids Research web site, http://nar.oupjournals.org/. PMID:15608247

Galperin, Michael Y.

2005-01-01

228

Comparing the public and private sequencing projects, Craig VenterSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Interviewee: Craig Venter DNAi Location:Genome>the project>players>private project Comparing public and private Craig Venter, the leader of the private genome effort at Celera Genomics, talks about the differences between the public and private approaches.

2008-10-06

229

Scientists Report New Online Cancer Research Databases  

Cancer.gov

Like the old saying "art for art's sake," most medical researchers once believed that creating large computer databases of known genes or DNA sequences was a case of gathering information for the sake of gathering information.

230

Bioconductor: annotation databases Thomas Lumley  

E-print Network

Bioconductor: annotation databases Thomas Lumley Ken Rice UW Biostatistics Seattle, June 2008 #12 chromosome, to estimate sex from DNA intensity and heterozygous X- chromosome loci, for QC. > head but tedious, so we want an automated approach #12;Example: finding chromosomes First extract the gene names

Rice, Ken

231

Database for sensorineural hearing loss  

Microsoft Academic Search

We are creating a bank of EBV immortalized lymphoblast cells and extracted DNA taken from the blood of deaf children and their relatives, in order to study the molecular basis of hereditary deafness. We have established a corresponding database for sensorineural hearing loss that records clinical data for each entered specimen. The purpose of this paper is to present the

Andrew J. Fishman; Nancy Sculerati

1996-01-01

232

Trail Database  

NSDL National Science Digital Library

Something of a veteran by Internet standards, the Trail Database has been around since 1997 and, as such, now bills itself as the "world's largest hiking trail database." "Henk," the Dutch hiker responsible for this compendium, updates the site regularly and has included a wide variety of links to helpful material here. Users can search or browse the resources, which are arranged both under general topics, such as Knots or Equipment, and by country. Those planning European hikes will find the links off the front page to foot and mouth disease-related hiking restrictions useful (though we found some of these links to be broken). In all, an impressive collection of material. The site is available in Dutch or English.

1997-01-01

233

CBS Databases  

NSDL National Science Digital Library

This major reference center for mycologists traces its existence back to 1903. Now an institute of the Royal Netherlands Academy of Arts and Sciences, CBS (Centraalbureau voor Schimmelcultures) continues to maintain and distribute one of the largest collections of living fungi in the world. With over 35,000 strains, "the collection contains representatives of virtually all fungal groups that can be cultured." Users can currently search six databases containing over 72,000 strains of fungi, yeasts, and bacteria held at CBS or other institutions. Each database offers several search options, such as by Species Name, Strain Number, or Properties of species/ strains. Search returns include Species, Variety, relevant Literature, Strain Number, Origin, History, and Form of Supply. The site also offers articles in HTML and .pdf format, information on current research themes and projects, strain ordering information, and an image gallery.

234

Avibase: The World Bird Database  

NSDL National Science Digital Library

This database provides information on all birds of the world, featuring information on thousands of species and subspecies of birds such as taxonomy, names and synonyms in various languages, photos, distribution maps, and links to additional information from other websites. The database is searchable by keyword or term, exact name, language, year of publication, and other parameters. There is also a search by taxonomic family, a set of checklists by geographic region, and a blog for ornithological discussions.

Lepage, Denis

235

The EMBL Nucleotide Sequence Database  

Microsoft Academic Search

The EMBL Nucleotide Sequence Database (http:\\/\\/ www.ebi.ac.uk\\/embl), maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK, is a comprehensive collection of nucleotide sequences and annotation from available public sources. The database is part of an international collaboration with DDBJ (Japan) and GenBank (USA). Data are exchanged daily between the collaborating institutes toachieveswiftsynchrony.Webinisthepreferredtool for individual submissions of nucleotide sequences, including

Carola Kanz; Philippe Aldebert; Nicola Althorpe; Wendy Baker; Alastair Baldwin; Kirsty Bates; Paul Browne; Alexandra Van Den Broek; Matias Castro; Guy Cochrane; Karyn Duggan; Ruth Eberhardt; Nadeem Faruque; John Gamble; Federico Garcia Diez; Nicola Harte; Tamara Kulikova; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Michelle Mchale; Francesco Nardone; Ville Silventoinen; Siamak Sobhany; Peter Stoehr; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler

2005-01-01

236

DNA Barcoding  

NSDL National Science Digital Library

This is a two-part animation. ÃÂDNA Barcoding, Part 1,ÃÂ provides an overview of how DNA barcoding of animals can be used to identify an unknown sample or discover a new species. Cytochrome c oxidase subunit 1 (COI) is found in the mitochondria as part of the electron transport chain. The COI gene is used for DNA barcoding. Just like a barcode on an item in a grocery store identifies a product, a DNA barcode (determined by DNA sequencing) is used to identify species. Part 1 run time: 1 minute, 40 seconds. ÃÂDNA Barcoding, Part 2ÃÂ details how small tissue samples are used for DNA barcoding, including a review of the laboratory and bioinformatics steps used in barcoding: DNA purification, polymerase chain reaction (PCR), agarose gel electrophoresis, DNA sequencing and analysis, and DNA sequence identification using the Basic Local Alignment Search Tool (BLAST) or the Barcode of Life Database (BOLD). Part 2 run time: 4 minutes, 15 seconds. Animation is closed captioned.

2012-10-22

237

PAH Mutation Analysis Consortium Database: 1997. Prototype for relational locus-specific mutation databases.  

PubMed Central

PAHdb (http://www.mcgill.ca/pahdb ) is a curated relational database (Fig. 1) of nucleotide variation in the human PAH cDNA (GenBank U49897). Among 328 different mutations by state (Fig. 2) the majority are rare mutations causing hyperphenylalaninemia (HPA) (OMIM 261600), the remainder are polymorphic variants without apparent effect on phenotype. PAHdb modules contain mutations, polymorphic haplotypes, genotype-phenotype correlations, expression analysis, sources of information and the reference sequence; the database also contains pages of clinical information and data on three ENU mouse orthologues of human HPA. Only six different mutations account for 60% of human HPA chromosomes worldwide, mutations stratify by population and geographic region, and the Oriental and Caucasian mutation sets are different (Fig. 3). PAHdb provides curated electronic publication and one third of its incoming reports are direct submissions. Each different mutation receives a systematic (nucleotide) name and a unique identifier (UID). Data are accessed both by a Newsletter and a search engine on the website; integrity of the database is ensured by keeping the curated template offline. There have been >6500 online interrogations of the website. PMID:9399840

Nowacki, P M; Byck, S; Prevost, L; Scriver, C R

1998-01-01

238

The AAVSO International Database  

NASA Astrophysics Data System (ADS)

The AAVSO International Database contains over 13 million variable star brightness estimates for nearly 10,000 known and suspected variable stars contributed by over 7300 observers since 1911. Data for some stars even date back as far as 1845. The database continues to grow, with over 700,000 new data points added in the last year. The database exists thanks to the dedication of the many tireless amateur and professional observers around the globe. This list of observers includes both well known names of the past and those who will no doubt become the well known names of the future. The AAVSO has a number of systems in place to ensure accuracy, such as: training for observers, standardized AAVSO charts, automated data entry checks, and data validation by AAVSO staff. The AAVSO is also committed to making the database accessible to the public. Raw observations are currently available in near real-time via the online data request form, light curve generator, and quick look file of recent observations. Multiple data formats are supported, including NVO standards.

Turner, Rebecca; Price, A.; Templeton, M.; Waagen, E. O.; Henden, A.

2006-12-01

239

The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database  

SciTech Connect

Background: With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes. Methodology/Principal Findings: A set of ~;;30K unique sequences (UniSeqs) representing ~;;19K clusters were generated from ~;;98K high quality ESTs from a set of tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66percent of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases.Conclusions/Significance: The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. Our assembly and clustering results suggest that our porcelain crab EST data set is equally diverse to the much larger EST set generated in the Daphnia pulex genome sequencing project, and thus will be an important resource to the Daphnia research community. Our homology results support the pancrustacea hypothesis and suggest that Malacostraca may be ancestral to Branchiopoda and Hexapoda. Our results also suggest that our cDNA microarrays cover as much of the transcriptome as can reasonably be captured in EST library sequencing approaches, and thus represent a rich resource for studies of environmental genomics.

Tagmount, Abderrahmane; Wang, Mei; Lindquist, Erika; Tanaka, Yoshihiro; Teranishi, Kristen S.; Sunagawa, Shinichi; Wong, Mike; Stillman, Jonathon H.

2010-01-27

240

The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection  

PubMed Central

The 20th annual Database Issue of Nucleic Acids Research includes 176 articles, half of which describe new online molecular biology databases and the other half provide updates on the databases previously featured in NAR and other journals. This year’s highlights include two databases of DNA repeat elements; several databases of transcriptional factors and transcriptional factor-binding sites; databases on various aspects of protein structure and protein–protein interactions; databases for metagenomic and rRNA sequence analysis; and four databases specifically dedicated to Escherichia coli. The increased emphasis on using the genome data to improve human health is reflected in the development of the databases of genomic structural variation (NCBI’s dbVar and EBI’s DGVa), the NIH Genetic Testing Registry and several other databases centered on the genetic basis of human disease, potential drugs, their targets and the mechanisms of protein–ligand binding. Two new databases present genomic and RNAseq data for monkeys, providing wealth of data on our closest relatives for comparative genomics purposes. The NAR online Molecular Biology Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, has been updated and currently lists 1512 online databases. The full content of the Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). PMID:23203983

Fernandez-Suarez, Xose M.; Galperin, Michael Y.

2013-01-01

241

NBRP databases: databases of biological resources in Japan  

PubMed Central

The National BioResource Project (NBRP) is a Japanese project that aims to establish a system for collecting, preserving and providing bioresources for use as experimental materials for life science research. It is promoted by 27 core resource facilities, each concerned with a particular group of organisms, and by one information center. The NBRP database is a product of this project. Thirty databases and an integrated database-retrieval system (BioResource World: BRW) have been created and made available through the NBRP home page (http://www.nbrp.jp). The 30 independent databases have individual features which directly reflect the data maintained by each resource facility. The BRW is designed for users who need to search across several resources without moving from one database to another. BRW provides access to a collection of 4.5-million records on bioresources including wild species, inbred lines, mutants, genetically engineered lines, DNA clones and so on. BRW supports summary browsing, keyword searching, and searching by DNA sequences or gene ontology. The results of searches provide links to online requests for distribution of research materials. A circulation system allows users to submit details of papers published on research conducted using NBRP resources. PMID:19934255

Yamazaki, Yukiko; Akashi, Ryo; Banno, Yutaka; Endo, Takashi; Ezura, Hiroshi; Fukami-Kobayashi, Kaoru; Inaba, Kazuo; Isa, Tadashi; Kamei, Katsuhiko; Kasai, Fumie; Kobayashi, Masatomo; Kurata, Nori; Kusaba, Makoto; Matuzawa, Tetsuro; Mitani, Shohei; Nakamura, Taro; Nakamura, Yukio; Nakatsuji, Norio; Naruse, Kiyoshi; Niki, Hironori; Nitasaka, Eiji; Obata, Yuichi; Okamoto, Hitoshi; Okuma, Moriya; Sato, Kazuhiro; Serikawa, Tadao; Shiroishi, Toshihiko; Sugawara, Hideaki; Urushibara, Hideko; Yamamoto, Masatoshi; Yaoita, Yoshio; Yoshiki, Atsushi; Kohara, Yuji

2010-01-01

242

Searching bibliographic databases for literature on chronic disease and work participation  

Microsoft Academic Search

Results The number of relevant publications retrieved from each database varied. Most (84%) of the relevant publications that were retrieved from each database were unique to that source. For each database, specific search terms for the concept of 'work' were useful for retrieving relevant publications. Conclusion Medline, EMBASE and PsycINFO are useful databases for quick searches. Useful search terms for

Joke Haafkens; Clara Moerman; Merel Schuring; Dijk van F. J. H

2006-01-01

243

Generation and Analysis of a Large-Scale Expressed Sequence Tag Database from a Full-Length Enriched cDNA Library of Developing Leaves of Gossypium hirsutum L  

PubMed Central

Background Cotton (Gossypium hirsutum L.) is one of the world’s most economically-important crops. However, its entire genome has not been sequenced, and limited resources are available in GenBank for understanding the molecular mechanisms underlying leaf development and senescence. Methodology/Principal Findings In this study, 9,874 high-quality ESTs were generated from a normalized, full-length cDNA library derived from pooled RNA isolated from throughout leaf development during the plant blooming stage. After clustering and assembly of these ESTs, 5,191 unique sequences, representative 1,652 contigs and 3,539 singletons, were obtained. The average unique sequence length was 682 bp. Annotation of these unique sequences revealed that 84.4% showed significant homology to sequences in the NCBI non-redundant protein database, and 57.3% had significant hits to known proteins in the Swiss-Prot database. Comparative analysis indicated that our library added 2,400 ESTs and 991 unique sequences to those known for cotton. The unigenes were functionally characterized by gene ontology annotation. We identified 1,339 and 200 unigenes as potential leaf senescence-related genes and transcription factors, respectively. Moreover, nine genes related to leaf senescence and eleven MYB transcription factors were randomly selected for quantitative real-time PCR (qRT-PCR), which revealed that these genes were regulated differentially during senescence. The qRT-PCR for three GhYLSs revealed that these genes express express preferentially in senescent leaves. Conclusions/Significance These EST resources will provide valuable sequence information for gene expression profiling analyses and functional genomics studies to elucidate their roles, as well as for studying the mechanisms of leaf development and senescence in cotton and discovering candidate genes related to important agronomic traits of cotton. These data will also facilitate future whole-genome sequence assembly and annotation in G. hirsutum and comparative genomics among Gossypium species. PMID:24146870

Pang, Chaoyou; Fan, Shuli; Song, Meizhen; Yu, Shuxun

2013-01-01

244

MycoperonDB: a database of computationally identified operons and transcriptional units in Mycobacteria  

PubMed Central

Background A key post genomics challenge is to identify how genes in an organism come together and perform physiological functions. An important first step in this direction is to identify transcriptional units, operons and regulons in a genome. Here we implement and report a strategy to computationally identify transcriptional units and operons of mycobacteria and construct a database-MycoperonDB. Description We have predicted transcriptional units and operons in mycobacteria and organized these predictions in the form of relational database called MycoperonDB. MycoperonDB database at present consists of 18053 genes organized as 8256 predicted operons and transcriptional units from five closely related species of mycobacteria. The database further provides literature links for experimentally characterized operons. All known promoters and related information is collected, analysed and stored. It provides a user friendly interface to allow a web based navigation of transcription units and operons. The web interface provides search tools to locate transcription factor binding DNA motif upstream to various genes. The reliability of operon prediction has been assessed by comparing the predicted operons with a set of known operons. Conclusion MycoperonDB is a publicly available structured relational database which has information about mycobacterial genes, transcriptional units and operons. We expect this database to assist molecular biologists/microbiologists in general, to hypothesize functional linkages between operonic genes of mycobacteria, their experimental characterization and validation. The database is freely available from our website . PMID:17254314

Ranjan, Sarita; Gundu, Ranjit Kumar; Ranjan, Akash

2006-01-01

245

Publication Bias in Antipsychotic Trials: An Analysis of Efficacy Comparing the Published Literature to the US Food and Drug Administration Database  

PubMed Central

Background Publication bias compromises the validity of evidence-based medicine, yet a growing body of research shows that this problem is widespread. Efficacy data from drug regulatory agencies, e.g., the US Food and Drug Administration (FDA), can serve as a benchmark or control against which data in journal articles can be checked. Thus one may determine whether publication bias is present and quantify the extent to which it inflates apparent drug efficacy. Methods and Findings FDA Drug Approval Packages for eight second-generation antipsychotics—aripiprazole, iloperidone, olanzapine, paliperidone, quetiapine, risperidone, risperidone long-acting injection (risperidone LAI), and ziprasidone—were used to identify a cohort of 24 FDA-registered premarketing trials. The results of these trials according to the FDA were compared with the results conveyed in corresponding journal articles. The relationship between study outcome and publication status was examined, and effect sizes derived from the two data sources were compared. Among the 24 FDA-registered trials, four (17%) were unpublished. Of these, three failed to show that the study drug had a statistical advantage over placebo, and one showed the study drug was statistically inferior to the active comparator. Among the 20 published trials, the five that were not positive, according to the FDA, showed some evidence of outcome reporting bias. However, the association between trial outcome and publication status did not reach statistical significance. Further, the apparent increase in the effect size point estimate due to publication bias was modest (8%) and not statistically significant. On the other hand, the effect size for unpublished trials (0.23, 95% confidence interval 0.07 to 0.39) was less than half that for the published trials (0.47, 95% confidence interval 0.40 to 0.54), a difference that was significant. Conclusions The magnitude of publication bias found for antipsychotics was less than that found previously for antidepressants, possibly because antipsychotics demonstrate superiority to placebo more consistently. Without increased access to regulatory agency data, publication bias will continue to blur distinctions between effective and ineffective drugs. Please see later in the article for the Editors' Summary PMID:22448149

Turner, Erick H.; Knoepflmacher, Daniel; Shapley, Lee

2012-01-01

246

Scientific publications about DNA structure-function and PCR technique in Costa Rica: A historic view (1953-2003)  

Microsoft Academic Search

The spreading of knowledge depends on the access to the information and its immediate use. Models are useful to explain specific phenomena. The scientific community accepts some models in Biology after a peri- od of time, once it has evidence to support it. The model of the structure and function of the DNA proposed by Watson & Crick (1953) was

Federico J. Albertazzi

247

A Chronostratigraphic Relational Database Ontology  

NASA Astrophysics Data System (ADS)

A chronostratigraphic research database was donated by British Petroleum to the Stratigraphy Group at the Energy and Geoscience Institute (EGI), University of Utah. These data consists of over 2,000 measured sections representing over three decades of research into the application of the graphic correlation method. The data are global and includes both microfossil (foraminifera, calcareous nannoplankton, spores, pollen, dinoflagellate cysts, etc) and macrofossil data. The objective of the donation was to make the research data available to the public in order to encourage additional chronostratigraphy studies, specifically regarding graphic correlation. As part of the National Science Foundation's Cyberinfrastructure for the Geosciences (GEON) initiative these data have been made available to the public at http://css.egi.utah.edu. To encourage further research using the graphic correlation method, EGI has developed a software package, StrataPlot that will soon be publicly available from the GEON website as a standalone software download. The EGI chronostratigraphy research database, although relatively large, has many data holes relative to some paleontological disciplines and geographical areas, so the challenge becomes how do we expand the data available for chronostratigrahic studies using graphic correlation. There are several public or soon-to-be public databases available to chronostratigraphic research, but they have their own data structures and modes of presentation. The heterogeneous nature of these database schemas hinders their integration and makes it difficult for the user to retrieve and consolidate potentially valuable chronostratigraphic data. The integration of these data sources would facilitate rapid and comprehensive data searches, thus helping advance studies in chronostratigraphy. The GEON project will host a number of databases within the geology domain, some of which contain biostratigraphic data. Ontologies are being developed to provide an integrated query system for the searching across GEON's biostratigraphy databases, as well as databases available in the public domain. Although creating an ontology directly from the existing database metadata would have been effective and straightforward, our effort was directed towards creating a more efficient representation of our database, as well as a general representation of the biostratigraphic domain.

Platon, E.; Gary, A.; Sikora, P.

2005-12-01

248

Comparative analysis of IRF6 variants in families with Van der Woude syndrome and popliteal pterygium syndrome using public whole-exome databases  

PubMed Central

Purpose: Mutations in the transcription factor IRF6 cause allelic autosomal dominant clefting syndromes, Van der Woude syndrome, and popliteal pterygium syndrome. We compared the distribution of IRF6 coding and splice-site mutations from 549 families with Van der Woude syndrome or popliteal pterygium syndrome with that of variants from the 1000 Genomes and National Heart, Lung, and Blood Institute Exome Sequencing Projects. Methods: We compiled all published pathogenic IRF6 mutations and performed direct sequencing of IRF6 in families with Van der Woude syndrome or popliteal pterygium syndrome. Results: Although mutations causing Van der Woude syndrome or popliteal pterygium syndrome were nonrandomly distributed with significantly increased frequencies in the DNA-binding domain (P = 0.0001), variants found in controls were rare and evenly distributed in IRF6. Of 194 different missense or nonsense variants described as potentially pathogenic, we identified only two in more than 6,000 controls. PolyPhen and SIFT (sorting intolerant from tolerant) reported 5.9% of missense mutations in patients as benign, suggesting that use of current in silico prediction models to determine function can have significant false negatives. Conclusion: Mutation of IRF6 occurs infrequently in controls, suggesting that for IRF6 there is a high probability that disruption of the coding sequence, particularly the DNA-binding domain, will result in syndromic features. Prior associations of coding sequence variants in IRF6 with clefting syndromes have had few false positives. PMID:23154523

Leslie, Elizabeth J.; Standley, Jennifer; Compton, John; Bale, Sherri; Schutte, Brian C.; Murray, Jeffrey C.

2013-01-01

249

Use of National Health Insurance database to evaluate the impact of public varicella vaccination program on burden of varicella in Taiwan  

Microsoft Academic Search

The aims of this study were to investigate the epidemiology of varicella and evaluate the effect of varicella vaccination on the burden of varicella in Taiwan. The outpatient and hospitalization claims made to the National Health Insurance (NHI) in public and private vaccination areas were compared during 2000–2002. In 2002, the outpatient visit rates for 1- to 5-year-old children in

Hung-Fu Tseng; Hsiu-Fen Tan; Chen-Kang Chang

2006-01-01

250

Stackfile Database  

NASA Technical Reports Server (NTRS)

This software provides storage retrieval and analysis functionality for managing satellite altimetry data. It improves the efficiency and analysis capabilities of existing database software with improved flexibility and documentation. It offers flexibility in the type of data that can be stored. There is efficient retrieval either across the spatial domain or the time domain. Built-in analysis tools are provided for frequently performed altimetry tasks. This software package is used for storing and manipulating satellite measurement data. It was developed with a focus on handling the requirements of repeat-track altimetry missions such as Topex and Jason. It was, however, designed to work with a wide variety of satellite measurement data [e.g., Gravity Recovery And Climate Experiment -- GRACE). The software consists of several command-line tools for importing, retrieving, and analyzing satellite measurement data.

deVarvalho, Robert; Desai, Shailen D.; Haines, Bruce J.; Kruizinga, Gerhard L.; Gilmer, Christopher

2013-01-01

251

Algaline Database  

NSDL National Science Digital Library

Maintained by the Finnish Institute of Marine Research and several other institutions, the Algaline Database offers updated reports on the conditions of phytoplankton and related parameters in the Baltic Sea. The reports, which vary in length and detail (though most are brief), summarize measurements of Oxygen, Salinity, Temperature, Nutrients, Harmful substances, Plankton, Zooplankton, Benthic Animals, Flow, and Other measurements. In addition, the Maps and Figures section offers numerous color images (including satellite) of Baltic Sea conditions and marine organisms. To access reports by geographic subregion of the Baltic, head to the Reports section. Finally, the Latest News section keeps researchers abreast of changing conditions (e.g., algal blooms) and research cruises in the Baltic. For researchers or anyone else wanting in-depth information on a host of ecological parameters for the Baltic Sea, this is an excellent reference site.

252

Missionary Periodicals Database  

NSDL National Science Digital Library

Hosted by the Yale Divinity School and created by the Currents in World Christianity Center at the University of Cambridge, this site is an amazing resource for anyone studying British missionary movements, religion, or the British empire. Visitors can browse the database by region or periodical title, or conduct a keyword search. Initial returns include title, issuing body, denomination, place, and dates of publication. Full entries include publisher, volume numbers, frequency, circulation, price, region of work, features, and some comments. Scholars who study these materials will undoubtedly make great use of this site.

253

Lighthouse Explorer Database  

NSDL National Science Digital Library

Spotted by ResearchBuzz, this site from the Lighthouse Depot, a "virtual community" (and store) for lighthouse enthusiasts, contains a database with information on over 1,300 lighthouses around the world. Visitors may browse the listings alphabetically, by category, by state or country, or search by keyword. Entries include name, location, supervising organization, contact information, email and Website when available, and in some cases a photo. Other useful information is also provided when available, such as the dates the lighthouse was built and operational, whether or not it is open to the public, and driving directions.

1995-01-01

254

Transboundary Freshwater Dispute Database  

NSDL National Science Digital Library

The database includes 150 water related treaties and 39 US compacts. The International Treaties and Compacts section is searchable by nation, basin, issues, conflict resolution mechanisms, non-water linkages, and date. US Compacts are searchable by state, basin, focus and date. For all treaties or compacts there is a summary of the agreement, the parties involved, allocations if applicable and other information pertinent to a specific agreement. There is also information available on indigenous approaches to water conflict resolution, a digitized inventory of the world's river basins with data about those basins, and a bibliography featuring publications about transboundary freshwater dispute resolution.

255

FishMicrosat: a microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent  

PubMed Central

Background Microsatellite DNA is one of many powerful genetic markers used for the construction of genetic linkage maps and the study of population genetics. The biological databases in public domain hold vast numbers of microsatellite sequences for many organisms including fishes. The microsatellite data available in these data sources were extracted and managed into a database that facilitates sequences analysis and browsing relevant information. The system also helps to design primer sequences for flanking regions of repeat loci for PCR identification of polymorphism within populations. Description FishMicrosat is a database of microsatellite sequences of fishes and shellfishes that includes important aquaculture species such as Lates calcarifer, Ctenopharyngodon idella, Hypophthalmichthys molitrix, Penaeus monodon, Labeo rohita, Oreochromis niloticus, Fenneropenaeus indicus and Macrobrachium rosenbergii. The database contains 4398 microsatellite sequences of 41 species belonging to 15 families from the Indian subcontinent. GenBank of NCBI was used as a prime data source for developing the database. The database presents information about simple and compound microsatellites, their clusters and locus orientation within sequences. The database has been integrated with different tools in a web interface such as primer designing, locus finding, mapping repeats, detecting similarities among sequences across species, and searching using motifs and keywords. In addition, the database has the ability to browse information on the top 10 families and the top 10 species, through record overview. Conclusions FishMicrosat database is a useful resource for fish and shellfish microsatellite analyses and locus identification across species, which has important applications in population genetics, evolutionary studies and genetic relatedness among species. The database can be expanded further to include the microsatellite data of fishes and shellfishes from other regions and available information on genome sequencing project of species of aquaculture importance. PMID:24047532

2013-01-01

256

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants  

PubMed Central

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops.

Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

2014-01-01

257

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants.  

PubMed

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

2014-09-01

258

ARTI refrigerant database  

SciTech Connect

The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alterative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on various refrigerants. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

Calm, J.M.

1997-02-01

259

ARTI refrigerant database  

SciTech Connect

The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufactures and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on many refrigerants including propane, ammonia, water, carbon dioxide, propylene, ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

Calm, J.M. [Calm (James M.), Great Falls, VA (United States)

1998-08-01

260

ARTI Refrigerant Database  

NASA Astrophysics Data System (ADS)

The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate the phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in the research and design of air-conditioning and refrigeration equipment. The complete documents are not included. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents to accelerate availability of the information and will be completed or replaced in future updates.

Cain, J. M.

1993-04-01

261

ARTI Refrigerant Database  

NASA Astrophysics Data System (ADS)

The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R134a, R-141b, R-142b, R-143a, R-152a, R-227ea, R-245ca, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyol ester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

Calm, J. M.

1993-11-01

262

ARTI Refrigerant Database  

SciTech Connect

The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents to accelerate availability of the information and will be completed or replaced in future updates.

Cain, J.M. (Calm (James M.), Great Falls, VA (United States))

1993-04-30

263

The urologic epithelial stem cell database (UESC) - a web tool for cell type-specific gene expression and immunohistochemistry images of the prostate and bladder  

PubMed Central

Background Public databases are crucial for analysis of high-dimensional gene and protein expression data. The Urologic Epithelial Stem Cells (UESC) database is a public database that contains gene and protein information for the major cell types of the prostate, prostate cancer cell lines, and a cancer cell type isolated from a primary tumor. Similarly, such information is available for urinary bladder cell types. Description Two major data types were archived in the database, protein abundance localization data from immunohistochemistry images, and transcript abundance data principally from DNA microarray analysis. Data results were organized in modules that were made to operate independently but built upon a core functionality. Gene array data and immunostaining images for human and mouse prostate and bladder were made available for interrogation. Data analysis capabilities include: (1) CD (cluster designation) cell surface protein data. For each cluster designation molecule, a data summary allows easy retrieval of images (at multiple magnifications). (2) Microarray data. Single gene or batch search can be initiated with Affymetrix Probeset ID, Gene Name, or Accession Number together with options of coalescing probesets and/or replicates. Conclusion Databases are invaluable for biomedical research, and their utility depends on data quality and user friendliness. UESC provides for database queries and tools to examine cell type-specific gene expression (normal vs. cancer), whereas most other databases contain only whole tissue expression datasets. The UESC database provides a valuable tool in the analysis of differential gene expression in prostate cancer genes in cancer progression. PMID:18072977

Pascal, Laura E; Deutsch, Eric W; Campbell, David S; Korb, Martin; True, Lawrence D; Liu, Alvin Y

2007-01-01

264

ADAM: another database of abbreviations in MEDLINE  

Microsoft Academic Search

Motivation: Abbreviations are an important type of terminology in the biomedical domain. Although several groups have already created databases of biomedical abbreviations, these are either not public, or are not comprehensive, or focus exclusively on acronym-type abbre- viations. We have created another abbreviation database, ADAM, which covers commonly used abbreviations and their definitions (or long-forms) within MEDLINE titles and abstracts,

Wei Zhou; Vetle I. Torvik; Neil R. Smalheiser

2006-01-01

265

Correlates of Access to Business Research Databases  

ERIC Educational Resources Information Center

This study examines potential correlates of business research database access through academic libraries serving top business programs in the United States. Results indicate that greater access to research databases is related to enrollment in graduate business programs, but not to overall enrollment or status as a public or private institution.…

Gottfried, John C.

2010-01-01

266

Development of steam generator vessel database  

Microsoft Academic Search

The purpose of this project was to collect publicly-available information on Steam Generator (SG) vessel integrity, abstract and summarize the information, and develop a database that could be used for identification of trends. The database developed includes information on 256 SGs (27 of them replacements for originally-installed SGs) in 75 operating Pressurized Water Reactor plants in the United States. The

R. K. Mattu; J. Lauderdale

1992-01-01

267

NICMOS HISTORY DATABASE AND April 10, 1998  

E-print Network

1 NICMOS HISTORY DATABASE AND WEB TOOLS C. Tullos April 10, 1998 ABSTRACT The history of NICMOS on the World Wide Web. The history tool which allows queries on the data, is available to the public. 1. The Database and Data A convenient way of keeping a history of some of the NICMOS instrument parameters

Sirianni, Marco

268

45 CFR 1356.80 - Scope of the National Youth in Transition Database.  

Code of Federal Regulations, 2011 CFR

...Scope of the National Youth in Transition Database. 1356.80 Section 1356.80 Public...Scope of the National Youth in Transition Database. The requirements of the National Youth in Transition Database (NYTD) §§ 1356.81 through...

2011-10-01

269

45 CFR 1356.80 - Scope of the National Youth in Transition Database.  

Code of Federal Regulations, 2013 CFR

...Scope of the National Youth in Transition Database. 1356.80 Section 1356.80 Public...Scope of the National Youth in Transition Database. The requirements of the National Youth in Transition Database (NYTD) §§ 1356.81 through...

2013-10-01

270

45 CFR 1356.80 - Scope of the National Youth in Transition Database.  

Code of Federal Regulations, 2010 CFR

...Scope of the National Youth in Transition Database. 1356.80 Section 1356.80 Public...Scope of the National Youth in Transition Database. The requirements of the National Youth in Transition Database (NYTD) §§ 1356.81 through...

2010-10-01

271

45 CFR 1356.80 - Scope of the National Youth in Transition Database.  

Code of Federal Regulations, 2012 CFR

...Scope of the National Youth in Transition Database. 1356.80 Section 1356.80 Public...Scope of the National Youth in Transition Database. The requirements of the National Youth in Transition Database (NYTD) §§ 1356.81 through...

2012-10-01

272

Overlap in Bibliographic Databases.  

ERIC Educational Resources Information Center

Examines the topic of Fuzzy Set Theory to determine the overlap of coverage in bibliographic databases. Highlights include examples of comparisons of database coverage; frequency distribution of the degree of overlap; records with maximum overlap; records unique to one database; intra-database duplicates; and overlap in the top ten databases.…

Hood, William W.; Wilson, Concepcion S.

2003-01-01

273

Mouse Resource Browser--a database of mouse databases  

PubMed Central

The laboratory mouse has become the organism of choice for discovering gene function and unravelling pathogenetic mechanisms of human diseases through the application of various functional genomic approaches. The resulting deluge of data has led to the deployment of numerous online resources and the concomitant need for formalized experimental descriptions, data standardization, database interoperability and integration, a need that has yet to be met. We present here the Mouse Resource Browser (MRB), a database of mouse databases that indexes 217 publicly available mouse resources under 22 categories and uses a standardised database description framework (the CASIMIR DDF) to provide information on their controlled vocabularies (ontologies and minimum information standards), and technical information on programmatic access and data availability. Focusing on interoperability and integration, MRB offers automatic generation of downloadable and re-distributable SOAP application-programming interfaces for resources that provide direct database access. MRB aims to provide useful information to both bench scientists, who can easily navigate and find all mouse related resources in one place, and bioinformaticians, who will be provided with interoperable resources containing data which can be mined and integrated. Database URL: http://bioit.fleming.gr/mrb PMID:20627861

Zouberakis, Michael; Chandras, Christina; Swertz, Morris; Smedley, Damian; Gruenberger, Michael; Bard, Jonathan; Schughart, Klaus; Rosenthal, Nadia; Hancock, John M.; Schofield, Paul N.; Kollias, George; Aidinis, Vassilis

2010-01-01

274

Molecular characterization of a cDNA encoding an excretory–secretory antigen from Toxocara canis second stage larvae and its application to the immunodiagnosis of human toxocariasis 1 The nucleotide sequence data reported in this paper appear in the DDBJ, EMBL and GenBank nucleotide sequence databases with the following accession number, AB009305. 1  

Microsoft Academic Search

The cDNA encoding an excretory–secretory antigen from the second stage larvae of Toxocara canis has been characterized. Sequence analysis revealed an open reading frame encoding a protein of 226 amino acid residues (Mr=24?398). Sequence database searches showed similarities to regions corresponding to epidermal growth factor-like and lectin-like domains of the core proteins of vertebrate chondroitin sulfate proteoglycans, which are major

Hiroshi Yamasaki; Radzan Taib; Yoh-ichi Watanabe; Joon Wah Mak; Ngah Zasmy; Kunioki Araki; Lim Patricia Kim Chooi; Kiyoshi Kita; Takashi Aoki

1998-01-01

275

RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers  

PubMed Central

Background Catalytic RNA molecules are called ribozymes. The aptamers are DNA or RNA molecules that have been selected from vast populations of random sequences, through a combinatorial approach known as SELEX. The selected oligo-nucleotide sequences (~200 bp in length) have the ability to recognize a broad range of specific ligands by forming binding pockets. These novel aptamer sequences can bind to nucleic acids, proteins or small organic and inorganic chemical compounds and have many potential uses in medicine and technology. Results The comprehensive sequence information on aptamers and ribozymes that have been generated by in vitro selection methods are included in this RiboaptDB database. Such types of unnatural data generated by in vitro methods are not available in the public 'natural' sequence databases such as GenBank and EMBL. The amount of sequence data generated by in vitro selection experiments has been accumulating exponentially. There are 370 artificial ribozyme sequences and 3842 aptamer sequences in the total 4212 sequences from 423 citations in this RiboaptDB. We included general search feature, and individual feature wise search, user submission form for new data through online and also local BLAST search. Conclusion This database, besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility in medicine, provides valuable information for computational and theoretical biologists. The RiboaptDB is extremely useful for garnering information about in vitro selection experiments as a whole and for better understanding the distribution of functional nucleic acids in sequence space. The database is updated regularly and is publicly available at . PMID:17118149

Thodima, Venkata; Pirooznia, Mehdi; Deng, Youping

2006-01-01

276

Environment Australia's Online Image Database  

NSDL National Science Digital Library

Environment Australia -- Australia's Department of Environment and Heritage -- has made its extensive collection of photographs freely available for non-commercial use. Researchers and students in the environmental sciences may find this collection of well-composed, high-quality images a useful resource for presentations and publications. Users may easily search the database by keyword, general subject, and/or geographic area. Search results yield a table of thumbnail photos together with summary information for each image. Before publishing an image from the database, users must first contact Environment Australia (via provided Web form).

277

The PAH mutation analysis consortium database: update 1996.  

PubMed Central

A website (http://www.mcgill.ca/pahdb ) is maintained by the curators for a Consortium (88 investigators, 28 countries) and all other users; it serves a relational database for human locus-specific genetic variation in a defined DNA sequence (GenBank U49897); (100 kb on human chromosome 12q24.1, gene symbol PAH). The intragenic nucleotide variation is both rare (Q< 0.01), extensive (>320 different mutations) and phenotype modifying, causing hyperphenylalaninemia by impairing phenylalanine hydroxylase function (see OMIM 261600), as well as polymorphic and neutral, the latter providing informative locus-specific haplotypes (>1200 different mutation/haplotype associations). The PAH database contains both offline core components (mutations, population associations and data source information) and several accessory online components: (i) relative frequencies of mutations by populations/regions (expanding file); (ii) data on genotype- phenotype correlations both in vitro and in vivo (new file); (iii) polymorphic haplotype structures (new file); (iv) intron sequence data (new file for design of primers); (v) description of mouse homologues (new file for mutations and phenotypes); (vi) the predicted PAH gene mutability profile (improved graphic); (vii) a clinical field for patient use (new interface with database). The website home page has been revised and a counter is recording >15 visits per day. Linkages to other mutation databases and an alliance of mutation database curators (new) are expanding. The primary 'electronic publication' reports now vastly exceed print reports. PAHdb serves as a prototype for obtaining, storing and distributing records of human genetic variation. PMID:9016524

Nowacki, P; Byck, S; Prevost, L; Scriver, C R

1997-01-01

278

National Residential Efficiency Measures Database  

DOE Data Explorer

The National Residential Efficiency Measures Database is a publicly available, centralized resource of residential building retrofit measures and costs for the U.S. building industry. With support from the U.S. Department of Energy, NREL developed this tool to help users determine the most cost-effective retrofit measures for improving energy efficiency of existing homes. Software developers who require residential retrofit performance and cost data for applications that evaluate residential efficiency measures are the primary audience for this database. In addition, home performance contractors and manufacturers of residential materials and equipment may find this information useful. The database offers the following types of retrofit measures: 1) Appliances, 2) Domestic Hot Water, 3) Enclosure, 4) Heating, Ventilating, and Air Conditioning (HVAC), 5) Lighting, 6) Miscellaneous.

279

World Database of Happiness  

NSDL National Science Digital Library

The World Database of Happiness, maintained by Professor Ruut Veenhoven of Erasmus University Rotterdam, is a "continuous register of scientific research on subjective appreciation of life." This site contains the Bibliography of Happiness, a collection of over 3,000 scientific publications accessible by author or subject; the Catalog of Happiness in Nations, providing responses from over 1,500 national happiness surveys taken in 93 different countries between 1946 and 1996; the Catalog of Happiness Correlates, which presents the abstracts of correlational research findings from 662 studies worldwide; and finally, the Directory of Happiness Investigators, an international listing of more than 3,300 happiness researchers. Users may freely download the Bibliography or the Catalog of Happiness in Nations as compressed MS Access files (.zip), and download the full text of the Catalog of Correlates in compressed RTF format (.zip).

280

Mouse phenome database.  

PubMed

The Mouse Phenome Database (MPD; phenome.jax.org) was launched in 2001 as the data coordination center for the international Mouse Phenome Project. MPD integrates quantitative phenotype, gene expression and genotype data into a common annotated framework to facilitate query and analysis. MPD contains >3500 phenotype measurements or traits relevant to human health, including cancer, aging, cardiovascular disorders, obesity, infectious disease susceptibility, blood disorders, neurosensory disorders, drug addiction and toxicity. Since our 2012 NAR report, we have added >70 new data sets, including data from Collaborative Cross lines and Diversity Outbred mice. During this time we have completely revamped our homepage, improved search and navigational aspects of the MPD application, developed several web-enabled data analysis and visualization tools, annotated phenotype data to public ontologies, developed an ontology browser and released new single nucleotide polymorphism query functionality with much higher density coverage than before. Here, we summarize recent data acquisitions and describe our latest improvements. PMID:24243846

Grubb, Stephen C; Bult, Carol J; Bogue, Molly A

2014-01-01

281

Alcohol Studies Database  

NSDL National Science Digital Library

Since 1987, staff members at the Rutgers University Center of Alcohol Studies have been collecting citations of documents related to alcohol. Today, they have over 80,000 citations and much of the material is related to research and professional materials that deal with the subject. Additionally, the database contains a small collection of educational and prevention materials designed for use by educators, parents, and public health workers. The site is maintained by the Scholarly Communication Center, the Center of Alcohol Studies, and the Rutgers University Libraries. Visitors to the site can search by subject, or perform a more advanced search as well. The site also includes a "Help" area, which includes information on limiting searches, links to full text, and suggestions on using Boolean techniques.

282

Reflective Database Access Control  

ERIC Educational Resources Information Center

"Reflective Database Access Control" (RDBAC) is a model in which a database privilege is expressed as a database query itself, rather than as a static privilege contained in an access control list. RDBAC aids the management of database access controls by improving the expressiveness of policies. However, such policies introduce new interactions…

Olson, Lars E.

2009-01-01

283

Database Management Certificate Program  

E-print Network

Database Management Certificate Program DATABASE TECHNOLOGIES 13 Today, organizations in every to obtain general data analysis and management skills or apply both Oracle and Microsoft SQL Server database capabilities of relational databases in conjunction with the new "Big Data" management frameworks for data

Rose, Michael R.

284

The DN A Database Search Controversy  

Microsoft Academic Search

SUMMARY. A recent article in Biometrics (Stockmarr, 1999, 55, 671-677) has generated correspondence (56, 1274-1277; 57, 976-980) reigniting a controversy started by a 1996 report on DNA profile evidence issued by the U.S. National Research Council (NRC). The issue concerns the evidential weight of a DNA profile match when the match results from a search through a profile database. The

David J. Balding

2002-01-01

285

Human sciences The human sciences database contains approximately 254 academic  

E-print Network

: (Public administration, economics, commerce, marketing, finance and banking, accountancy). Engineering and statistical reports on the following subjects: (Pathology, nutrition and diet, nursing, public health, education, psychology, arts, languages and Library Science) Social sciences The social sciences database

286

Challenges of DNA profiling in mass disaster investigations.  

PubMed

In cases of mass disaster, there is often a need for managing, analyzing, and comparing large numbers of biological samples and DNA profiles. This requires the use of laboratory information management systems for large-scale sample logging and tracking, coupled with bioinformatic tools for DNA database searching according to different matching algorithms, and for the evaluation of the significance of each match by likelihood ratio calculations. There are many different interrelated factors and circumstances involved in each specific mass disaster scenario that may challenge the final DNA identification goal, such as: the number of victims, the mechanisms of body destruction, the extent of body fragmentation, the rate of DNA degradation, the body accessibility for sample collection, or the type of DNA reference samples availability. In this paper, we examine the different steps of the DNA identification analysis (DNA sampling, DNA analysis and technology, DNA database searching, and concordance and kinship analysis) reviewing the "lessons learned" and the scientific progress made in some mass disaster cases described in the scientific literature. We will put special emphasis on the valuable scientific feedback that genetic forensic community has received from the collaborative efforts of several public and private USA forensic laboratories in assisting with the more critical areas of the World Trade Center (WTC) mass fatality of September 11, 2001. The main challenges in identifying the victims of the recent South Asian Tsunami disaster, which has produced the steepest death count rise in history, will also be considered. We also present data from two recent mass fatality cases that involved Spanish victims: the Madrid terrorist attack of March 11, 2004, and the Yakolev-42 aircraft accident in Trabzon, Turkey, of May 26, 2003. PMID:16100756

Alonso, Antonio; Martin, Pablo; Albarrán, Cristina; Garcia, Pilar; Fernandez de Simon, Lourdes; Jesús Iturralde, Maria; Fernández-Rodriguez, Amparo; Atienza, Inmaculada; Capilla, Javier; García-Hirschfeld, Julia; Martinez, Pilar; Vallejo, Gloria; García, Oscar; García, Emilio; Real, Pilar; Alvarez, David; León, Antonio; Sancho, Manuel

2005-08-01

287

VoSeq: a voucher and DNA sequence web application.  

PubMed

There is an ever growing number of molecular phylogenetic studies published, due to, in part, the advent of new techniques that allow cheap and quick DNA sequencing. Hence, the demand for relational databases with which to manage and annotate the amassing DNA sequences, genes, voucher specimens and associated biological data is increasing. In addition, a user-friendly interface is necessary for easy integration and management of the data stored in the database back-end. Available databases allow management of a wide variety of biological data. However, most database systems are not specifically constructed with the aim of being an organizational tool for researchers working in phylogenetic inference. We here report a new software facilitating easy management of voucher and sequence data, consisting of a relational database as back-end for a graphic user interface accessed via a web browser. The application, VoSeq, includes tools for creating molecular datasets of DNA or amino acid sequences ready to be used in commonly used phylogenetic software such as RAxML, TNT, MrBayes and PAUP, as well as for creating tables ready for publishing. It also has inbuilt BLAST capabilities against all DNA sequences stored in VoSeq as well as sequences in NCBI GenBank. By using mash-ups and calls to web services, VoSeq allows easy integration with public services such as Yahoo! Maps, Flickr, Encyclopedia of Life (EOL) and GBIF (by generating data-dumps that can be processed with GBIF's Integrated Publishing Toolkit). PMID:22720030

Peña, Carlos; Malm, Tobias

2012-01-01

288

On-Line Databases in Mexico.  

ERIC Educational Resources Information Center

Use of online bibliographic databases in Mexico is provided through Servicio de Consulta a Bancos de Informacion, a public service that provides information retrieval, document delivery, translation, technical support, and training services. Technical infrastructure is based on a public packet-switching network and institutional users may receive…

Molina, Enzo

1986-01-01

289

CEBAF Large Acceptance Spectrometer (CLAS) Physics Database  

DOE Data Explorer

A username and password are required to access and search the entire database. However, the Overview page provides links to detailed data pages for each of the experiments available for public access. There are many experiments with data that the public can freely access.

290

DNA sequence comparison based on amino acid similarity  

E-print Network

DNA databases are growing exponentially. Sequence similarities are often the most valuable information we can get from DNA databases. Especially for protein-coding sequences, comparison of translated sequences give us clues to protein function. However gaps in DNA sequences prevent us from translation and force us to compare them as they are. We present an algorithm for DNA sequence comparison which translates the sequences most reliably and compares the translated sequences. The method enables us to find protein sequence similarity in DNA sequences even if we do not know the protein sequences which are coded in the DNA sequences. 1 Introduction Most of protein sequences are determined from DNA sequences. DNA database size is increasing exponentially. If we can translate all protein-coding sequences in DNA databases it will make the most up-to-date protein databases. However translation is impossible for some of the sequences because of difficulty of predicting coding regions and alte...

Hiraoka Nagai; S. Hiraoka; K. Nagai

291

ppdb: a plant promoter database  

PubMed Central

ppdb (http://www.ppdb.gene.nagoya-u.ac.jp) is a plant promoter database that provides promoter annotation of Arabidopsis and rice. The database contains information on promoter structures, transcription start sites (TSSs) that have been identified from full-length cDNA clones and also a vast amount of TSS tag data. In ppdb, the promoter structures are determined by sets of promoter elements identified by a position-sensitive extraction method called local distribution of short sequences (LDSS). By using this database, the core promoter structure, the presence of regulatory elements and the distribution of TSS clusters can be identified. Although no differentiation of promoter architecture among plant species has been reported, there is some divergence of utilized sequences for promoter elements. Therefore, ppdb is based on species-specific sets of promoter elements, rather than on general motifs for multiple species. Each regulatory sequence is hyperlinked to literary information, a PLACE entry served by a plant cis-element database, and a list of promoters containing the regulatory sequence. PMID:17947329

Yamamoto, Yoshiharu Y.; Obokata, Junichi

2008-01-01

292

ppdb: a plant promoter database.  

PubMed

ppdb (http://www.ppdb.gene.nagoya-u.ac.jp) is a plant promoter database that provides promoter annotation of Arabidopsis and rice. The database contains information on promoter structures, transcription start sites (TSSs) that have been identified from full-length cDNA clones and also a vast amount of TSS tag data. In ppdb, the promoter structures are determined by sets of promoter elements identified by a position-sensitive extraction method called local distribution of short sequences (LDSS). By using this database, the core promoter structure, the presence of regulatory elements and the distribution of TSS clusters can be identified. Although no differentiation of promoter architecture among plant species has been reported, there is some divergence of utilized sequences for promoter elements. Therefore, ppdb is based on species-specific sets of promoter elements, rather than on general motifs for multiple species. Each regulatory sequence is hyperlinked to literary information, a PLACE entry served by a plant cis-element database, and a list of promoters containing the regulatory sequence. PMID:17947329

Yamamoto, Yoshiharu Y; Obokata, Junichi

2008-01-01

293

Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead.  

PubMed

Ten years after DNA barcoding was initially suggested as a tool to identify species, millions of barcode sequences from more than 1100 species are available in public databases. While several studies have reviewed the methods and potential applications of DNA barcoding, most have focused on species identification and discovery, and relatively few have addressed applications of DNA barcoding data to ecology. These data, and the associated information on the evolutionary histories of taxa that they can provide, offer great opportunities for ecologists to investigate questions that were previously difficult or impossible to address. We present an overview of potential uses of DNA barcoding relevant in the age of ecoinformatics, including applications in community ecology, species invasion, macroevolution, trait evolution, food webs and trophic interactions, metacommunities, and spatial ecology. We also outline some of the challenges and potential advances in DNA barcoding that lie ahead. PMID:24118947

Joly, Simon; Davies, T Jonathan; Archambault, Annie; Bruneau, Anne; Derry, Alison; Kembel, Steven W; Peres-Neto, Pedro; Vamosi, Jana; Wheeler, Terry A

2014-03-01

294

Curation accuracy of model organism databases  

PubMed Central

Manual extraction of information from the biomedical literature—or biocuration—is the central methodology used to construct many biological databases. For example, the UniProt protein database, the EcoCyc Escherichia coli database and the Candida Genome Database (CGD) are all based on biocuration. Biological databases are used extensively by life science researchers, as online encyclopedias, as aids in the interpretation of new experimental data and as golden standards for the development of new bioinformatics algorithms. Although manual curation has been assumed to be highly accurate, we are aware of only one previous study of biocuration accuracy. We assessed the accuracy of EcoCyc and CGD by manually selecting curated assertions within randomly chosen EcoCyc and CGD gene pages and by then validating that the data found in the referenced publications supported those assertions. A database assertion is considered to be in error if that assertion could not be found in the publication cited for that assertion. We identified 10 errors in the 633 facts that we validated across the two databases, for an overall error rate of 1.58%, and individual error rates of 1.82% for CGD and 1.40% for EcoCyc. These data suggest that manual curation of the experimental literature by Ph.D-level scientists is highly accurate. Database URL: http://ecocyc.org/, http://www.candidagenome.org// PMID:24923819

Keseler, Ingrid M.; Skrzypek, Marek; Weerasinghe, Deepika; Chen, Albert Y.; Fulcher, Carol; Li, Gene-Wei; Lemmer, Kimberly C.; Mladinich, Katherine M.; Chow, Edmond D.; Sherlock, Gavin; Karp, Peter D.

2014-01-01

295

Current trends in publicly available genetic databases  

Microsoft Academic Search

Analysis of human genetic data promises to uncover important disease targets. Genes known to cause or increase susceptibility for various diseases are being identified through analysis of genetic data, expression and metabolites. Future benefits to individuals are far-reaching, including improved gene therapy strategies, better drug development for disease treatment, pre-symptomatic disease intervention and risk susceptibility information. The rapid expansion of

Michael G. Tyshenko; William Leiss

2005-01-01

296

Introduction to Database Database Systems Lecture 1  

E-print Network

" Dictionary.com #12;Databases · Web indexes · Library catalogues · Medical records · Bank accounts · Stock Dictionary - Metadata · The dictionary or catalog stores information about the database itself · This is data about data or `metadata' · Almost every aspect of the DBMS uses the dictionary · The dictionary holds

Alechina, Natasha

297

Search the PAQ Database  

Cancer.gov

Use this interface to search through all the physical activity-related questions in our database. See below for some tips on how to search. If you have any comments concerning this database, please e-mail David Berrigan.

298

NIOSH Power Tools Database  

MedlinePLUS

... Search Tool Type: Manufacturer: Technical Specifications: Power Tools Database Choose one of the tools below to view sound specifications. Disclaimer: The NIOSH database does not include a comprehensive list of manufacturers ...

299

The Chloroplast Function Database II: a comprehensive collection of homozygous mutants and their phenotypic/genotypic traits for nuclear-encoded chloroplast proteins.  

PubMed

The Chloroplast Function Database has so far offered phenotype information on mutants of the nuclear-encoded chloroplast proteins in Arabidopsis that pertains to >200 phenotypic data sets that were obtained from 1,722 transposon- or T-DNA-tagged lines. Here, we present the development of the second version of the database, which is named the Chloroplast Function Database II and was redesigned to increase the number of mutant characters and new user-friendly tools for data mining and integration. The upgraded database offers information on genome-wide mutant screens for any visible phenotype against 2,495 tagged lines to create a comprehensive homozygous mutant collection. The collection consists of 147 lines with seedling phenotypes and 185 lines for which we could not obtain homozygotes, as well as 1,740 homozygotes with wild-type phenotypes. Besides providing basic information about primer lists that were used for the PCR genotyping of T-DNA-tagged lines and explanations about the preparation of homozygous mutants and phenotype screening, the database includes access to a link between the gene locus and existing publicly available databases. This gives users access to a combined pool of data, enabling them to gain valuable insights into biological processes. In addition, high-resolution images of plastid morphologies of mutants with seedling-specific chloroplast defects as observed with transmission electron microscopy (TEM) are available in the current database. This database is used to compare the phenotypes of visually identifiable mutants with their plastid ultrastructures and to evaluate their potential significance from characteristic patterns of plastid morphology in vivo. Thus, the Chloroplast Function Database II is a useful and comprehensive information resource that can help researchers to connect individual Arabidopsis genes to plastid functions on the basis of phenotype analysis of our tagged mutant collection. It can be freely accessed at http://rarge.psc.riken.jp/chloroplast/. PMID:23230006

Myouga, Fumiyoshi; Akiyama, Kenji; Tomonaga, Yumi; Kato, Aya; Sato, Yuka; Kobayashi, Megumi; Nagata, Noriko; Sakurai, Tetsuya; Shinozaki, Kazuo

2013-02-01

300

MEPD: a Medaka gene expression pattern database.  

PubMed

The Medaka Expression Pattern Database (MEPD) stores and integrates information of gene expression during embryonic development of the small freshwater fish Medaka (Oryzias latipes). Expression patterns of genes identified by ESTs are documented by images and by descriptions through parameters such as staining intensity, category and comments and through a comprehensive, hierarchically organized dictionary of anatomical terms. Sequences of the ESTs are available and searchable through BLAST. ESTs in the database are clustered upon entry and have been blasted against public data-bases. The BLAST results are updated regularly, stored within the database and searchable. The MEPD is a project within the Medaka Genome Initiative (MGI) and entries will be interconnected to integrated genomic map databases. MEPD is accessible through the WWW at http://medaka.dsp.jst.go.jp/MEPD. PMID:12519950

Henrich, Thorsten; Ramialison, Mirana; Quiring, Rebecca; Wittbrodt, Beate; Furutani-Seiki, Makoto; Wittbrodt, Joachim; Kondoh, Hisato

2003-01-01

301

PRIDE: the proteomics identifications database.  

PubMed

The advent of high-throughput proteomics has enabled the identification of ever increasing numbers of proteins. Correspondingly, the number of publications centered on these protein identifications has increased dramatically. With the first results of the HUPO Plasma Proteome Project being analyzed and many other large-scale proteomics projects about to disseminate their data, this trend is not likely to flatten out any time soon. However, the publication mechanism of these identified proteins has lagged behind in technical terms. Often very long lists of identifications are either published directly with the article, resulting in both a voluminous and rather tedious read, or are included on the publisher's website as supplementary information. In either case, these lists are typically only provided as portable document format documents with a custom-made layout, making it practically impossible for computer programs to interpret them, let alone efficiently query them. Here we propose the proteomics identifications (PRIDE) database (http://www.ebi.ac.uk/pride) as a means to finally turn publicly available data into publicly accessible data. PRIDE offers a web-based query interface, a user-friendly data upload facility, and a documented application programming interface for direct computational access. The complete PRIDE database, source code, data, and support tools are freely available for web access or download and local installation. PMID:16041671

Martens, Lennart; Hermjakob, Henning; Jones, Philip; Adamski, Marcin; Taylor, Chris; States, David; Gevaert, Kris; Vandekerckhove, Joël; Apweiler, Rolf

2005-08-01

302

The UMIST database for astrochemistry 2006  

Microsoft Academic Search

Aims:We present a new version of the UMIST Database for Astrochemistry, the fourth such version to be released to the public. The current version contains some 4573 binary gas-phase reactions, an increase of 10% from the previous (1999) version, among 420 species, of which 23 are new to the database. Methods: Major updates have been made to ion-neutral reactions, neutral-neutral

J. Woodall; M. Agúndez; A. J. Markwick-Kemper; T. J. Millar

2007-01-01

303

EMBL Nucleotide Sequence Database: developments in 2005  

Microsoft Academic Search

The EMBL Nucleotide Sequence Database (www.ebi. ac.uk\\/embl) at the EMBL European Bioinformatics Institute, UK, offers a comprehensive set of publicly available nucleotide sequence and annotation, freely accessible to all. Maintained in collaboration with partners DDBJ and GenBank, coverage includes whole genome sequencing project data, directly sub- mitted sequence, sequence recorded in support of patent applications and much more. The database

Guy Cochrane; Philippe Aldebert; Nicola Althorpe; Mikael Andersson; Wendy Baker; Alastair Baldwin; Kirsty Bates; Sumit Bhattacharyya; Paul Browne; Alexandra Van Den Broek; Matias Castro; Karyn Duggan; Ruth Eberhardt; Nadeem Faruque; John Gamble; Carola Kanz; Tamara Kulikova; Charles Lee; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Michelle Mchale; Hamish Mcwilliam; Gaurab Mukherjee; Francesco Nardone; Maria Pilar Garcia Pastor; Siamak Sobhany; Peter Stoehr; Katerina Tzouvara; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler

2006-01-01

304

Using a FASTA Sequence Database Similarity Search.  

PubMed

INTRODUCTIONFASTA is a program for rapid alignment of pairs of protein and DNA sequences. Rather than comparing individual residues in the two sequences, FASTA searches for matching sequence patterns or words, called k-tuples. These patterns comprise k consecutive matches of letters in both sequences. The program then attempts to build a local alignment based on these word matches. Due to the ability of the algorithm to find matching sequences in a sequence database with high speed, FASTA is useful for routine database searches of this type. Comparable methods are the BLAST program, which is faster than FASTA, is of comparable sensitivity for protein queries, and also does DNA searches, and programs that use the Smith-Waterman dynamic programming algorithm for protein and DNA searches, which are slower but more sensitive when full-length protein sequences are used as queries. PMID:21357134

Mount, David W

2007-01-01

305

MPlus Database system  

SciTech Connect

The MPlus Database program was developed to keep track of mail received. This system was developed by TRESP for the Department of Energy/Oak Ridge Operations. The MPlus Database program is a PC application, written in dBase III+'' and compiled with Clipper'' into an executable file. The files you need to run the MPLus Database program can be installed on a Bernoulli, or a hard drive. This paper discusses the use of this database.

Not Available

1989-01-20

306

DHQ Database Revision History  

Cancer.gov

The following details all additions and revisions made to the DHQ nutrient and food database. This revision history is provided as a reference for investigators who may have performed analyses with a previous release of the database. The contents of the current database are listed in Nutrient and Dietary Constituents and Pyramid Food Groups.

307

Mission and Assets Database  

NASA Technical Reports Server (NTRS)

Mission and Assets Database (MADB) Version 1.0 is an SQL database system with a Web user interface to centralize information. The database stores flight project support resource requirements, view periods, antenna information, schedule, and forecast results for use in mid-range and long-term planning of Deep Space Network (DSN) assets.

Baldwin, John; Zendejas, Silvino; Gutheinz, Sandy; Borden, Chester; Wang, Yeou-Fang

2009-01-01

308

Database Encryption Luc Bouganim  

E-print Network

Database Encryption Luc Bouganim INRIA Rocquencourt Le Chesnay, FRANCE Luc.Bouganim@inria.fr Yanli GUO INRIA Rocquencourt Le Chesnay, FRANCE yanli.guo@inria.fr Related concepts and keywords Database security, Data confidentiality, Hardware Security Module Definition Database encryption refers to the use

309

ORACLE CERTIFICATION Oracle Database  

E-print Network

ORACLE CERTIFICATION Oracle Database Administration Certificate Program Train with the best. Get your Oracle Database Administration education from the number-one provider* of Oracle training-on, lab-based understanding of Oracle, the world's leading database platform, and long the product

Loudon, Catherine

310

USER'S GUIDE DATABASE SYSTEM  

E-print Network

USER'S GUIDE TO THE MINGL DATABASE SYSTEM FOR TFTR Version 4.1 R. M. Wieland Plasma Physics blank] #12;1 Abstract The MINGL database system is an integrated set of tools which is used to collect relational databases. A flexible software tool set makes it easy to browse, select, compare and display

311

16 CFR 1102.28 - Publication of reports of harm.  

Code of Federal Regulations, 2013 CFR

...AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102...the requirements for publication in the Database. The Commission will publish reports...requirements of § 1102.10(d) in the Database beyond the 10-business-day time...

2013-01-01

312

16 CFR 1102.28 - Publication of reports of harm.  

Code of Federal Regulations, 2012 CFR

...AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102...the requirements for publication in the Database. The Commission will publish reports...requirements of § 1102.10(d) in the Database beyond the 10-business-day time...

2012-01-01

313

16 CFR 1102.28 - Publication of reports of harm.  

...AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102...the requirements for publication in the Database. The Commission will publish reports...requirements of § 1102.10(d) in the Database beyond the 10-business-day time...

2014-01-01

314

DNA Sequencing apparatus  

DOEpatents

An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.

Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)

1992-01-01

315

Silicon Valley Companies Database (SV150)  

NSDL National Science Digital Library

Created by Mercury Center, the online service of the San Jose Mercury News, this database offers financial information and company background for the 150 largest publicly traded companies in Silicon Valley. Silicon Valley is defined as the cities of Santa Cruz and Santa Clara, as well as the southern sections of San Mateo and Alameda counties. The database is searchable by company name, stock symbol, 1997 sales, industry type, product, and location. Clear, detailed instructions will help users best use the database. The search results link to company homepages and charted stock prices.

316

University of Washington: Database Research Group  

NSDL National Science Digital Library

The University of Washington's Database Research Group âÂÂis focused on broadening the scope of database and data management techniques beyond their traditional scope.â Its work focuses on databases and the Web, XML, data management for ubiquitous computing, data integration, and data mining. For example, the Mangrove project seeks to facilitate the move to the semantic Web by creating âÂÂan environment in which users are motivated to create semantic content because of the existence of useful semantic services.â The various projects are described on this website along with related publications, which are available to download.

317

ETC Spills Technology Databases: Oil Properties Database  

NSDL National Science Digital Library

The Environmental Technology Center of Environment Canada provides a database which contains various properties of crude oils and petroleum products. In addition to the listing of oils, the database reports properties "which will likely determine the environmental behavior and effects of spilled oil." The user may select an oil from a pull-down menu that lists 412 oils. The data are organized into tables in the following areas: Origin, API Gravity, Density, Pour Point, Dynamic Viscosity, Hydrocarbon Groups, and Distillation.

Fieldhouse, B.; Fingas, M.; Jokuty, P.; Lambert, P.; Mullin, J.; Wang, Z.

318

Raintree: Tropical Plant Database  

NSDL National Science Digital Library

Hosted by Raintree, the Tropical Plant Database is authored and maintained by Board Certified Naturopath, Ms. Leslie Taylor to provide accurate information about rainforest plants and to help promote rainforest conservation. Including over 300 pages of documentation on rainforest plants and very well-organized, the Tropical Plant Database lists plants by Common name, Botanical name, Ethnic uses, and Action/disorder. The Database File for each plant includes an illustration and information about family, genus, species, common names, plant description, and more. Visitors can link to great illustrations and photos as well as web resources for each plant including Medline Abstracts, W3 TROPICOS Database, Ethnobotany Database, and Phtyochem Database among others. Plant Database File pages include references as well.

319

IPD--the Immuno Polymorphism Database.  

PubMed

The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors; IPD-MHC, a database of sequences of the Major Histocompatibility Complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC share the same database structure. The sharing of a common database structure makes it easier to implement common tools for data submission and retrieval. The data are currently available online from the website and ftp directory; files will also be made available in different formats to download from the website and ftp server. The data will also be included in SRS, BLAST and FASTA search engines at the European Bioinformatics Institute. PMID:15608253

Robinson, James; Waller, Matthew J; Stoehr, Peter; Marsh, Steven G E

2005-01-01

320

Measuring Heterogeneity in Forensic Databases Using Hierarchical Bayes Models  

E-print Network

Measuring Heterogeneity in Forensic Databases Using Hierarchical Bayes Models By Kathryn Roeder Corporation, 550 West Avenue, Stamford, CT 06902, U.S.A. October 25, 1995 Summary DNA fingerprint profiles, as currently defined, do not uniquely identify individuals. For criminal cases involving DNA evidence, forensic

321

Measuring Heterogeneity in Forensic Databases Using Hierarchical Bayes Models  

E-print Network

Measuring Heterogeneity in Forensic Databases Using Hierarchical Bayes Models By Kathryn Roeder Corporation, 550 West Avenue, Stamford, CT 06902, U.S.A. Revised August 1997 Summary DNA fingerprint profiles, as currently defined, do not uniquely identify individuals. For criminal cases involving DNA evidence, forensic

322

Information storage in DNA sequences  

SciTech Connect

We seek to describe a starting point for modeling the evolution of DNA sequences within the framework of cellular automata by discussing the current understanding of genetic information storage in DNA sequences. This includes alternately viewing the role of DNA in living organisms as a simple scheme and as a complex scheme; a presentation of the extent of experimentally determined DNA sequence data present in the Los Alamos Nucleic Acid Database; and finally, a brief review of strategies for identifying and classifying patterns in DNA sequences.

Burks, C.

1983-01-01

323

Forensic DNA analysis.  

PubMed

Before the routine use of DNA profiling, blood typing was an important forensic tool. However, blood typing was not very discriminating. For example, roughly 30% of the United States population has type A-positive blood. Therefore, if A-positive blood were found at a crime scene, it could have come from 30% of the population. DNA profiling has a much better ability for discrimination. Forensic laboratories no longer routinely determine blood type. If blood is found at a crime scene, DNA profiling is performed. From Jeffrey's discovery of DNA fingerprinting to the development of PCR of STRs to the formation of DNA databases, our knowledge of DNA and DNA profiling have expanded greatly. Also, the applications for which we use DNA profiling have increased. DNA profiling is not just used for criminal case work, but it has expanded to encompass paternity testing, disaster victim identification, monitoring bone marrow transplants, detecting fetal cells in a mother's blood, tracing human history, and a multitude of other areas. The future of DNA profiling looks expansive with the development of newer instrumentation and techniques. PMID:22693781

McDonald, Jessica; Lehman, Donald C

2012-01-01

324

Database description with SDM: a semantic database model  

Microsoft Academic Search

SDM is a high-level semantics-based database description and structuring formalism (database model) for databases. This database model is designed to capture more of the meaning of an application environment than is possible with contemporary database models. An SDM specification describes a database in terms of the kinds of entities that exist in the application environment, the classifications and groupings of

Michael M. Hammer; Dennis Mc Leod

1981-01-01

325

Database Description with SDM: A Semantic Database Model  

Microsoft Academic Search

SDM is a high-level semantics-based database description and structuring formalism (database model) for databases. This database model is designed to capture more of the meaning of an application environment than is possible with contemporary database models. An SDM specification describes a database in terms of the kinds of entities that exist in the application environment, the classifications and groupings of

Michael Hammer; Dennis Mcleod

1990-01-01

326

Testing Database-Centric Applications For Causes of Database Deadlocks  

E-print Network

Testing Database-Centric Applications For Causes of Database Deadlocks Mark Grechanik, B. M. Mainul--Many organizations deploy applications that use databases by sending Structured Query Language (SQL) state- ments the same databases concurrently, database deadlocks routinely occur in these databases. Testing

Grechanik, Mark

327

Database tool ASGARD: an open-access database of  

E-print Network

Database tool ASGARD: an open-access database of annotated transcriptomes for emerging model database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository include search term auto-completion sug- gestions based on database content, the ability to download

Extavour, Cassandra

328

Database Description with SDM: A Semantic Database Model  

E-print Network

Database Description with SDM: A Semantic Database Model MICHAEL HAMMER Massachusetts Institute of Technology and DENNIS McLEOD University of Southern California SDM is a high-level semantics-based database description and structuring formalism (database model) for databases. This database model is designed

McLeod, Dennis

329

Buffer Management in Distributed Database Systems: A Data MiningBased Approach ?  

E-print Network

Buffer Management in Distributed Database Systems: A Data Mining­Based Approach ? L. Feng 1 H. Lu 2­based approach to public buffer management in distributed database systems where database buffers are organized into two areas: public and private. While the private buffer areas contain pages to be updated

Tung, Anthony Kum Hoe

330

16 CFR 1102.30 - Publication of manufacturer comments.  

Code of Federal Regulations, 2012 CFR

...REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102.30 Publication of manufacturer...1102.24, and 1102.26, the Commission will publish in the Database manufacturer comments submitted in response to a report of...

2012-01-01

331

16 CFR 1102.30 - Publication of manufacturer comments.  

Code of Federal Regulations, 2013 CFR

...REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102.30 Publication of manufacturer...1102.24, and 1102.26, the Commission will publish in the Database manufacturer comments submitted in response to a report of...

2013-01-01

332

16 CFR 1102.30 - Publication of manufacturer comments.  

...REGULATIONS PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102.30 Publication of manufacturer...1102.24, and 1102.26, the Commission will publish in the Database manufacturer comments submitted in response to a report of...

2014-01-01

333

HGBASE: a database of SNPs and other variations in and around human genes  

PubMed Central

Human genome polymorphism is expected to play a key role in defining the etiologic basis of phenotypic differences between individuals in aspects such as drug responses and common disease predisposition. Relevant functional DNA changes will probably be located in or near to transcribed sequences, and include many single nucleotide polymorphisms. To aid the future analysis of such genome variation, HGBASE (Human Genic Bi-Allelic SEquences) was constructed as a means to gather human gene-linked polymorphisms from all possible public sources, and show these as a non-redundant set of records in a standardized and user-friendly database endowed with text and sequence based search facilities. After 1 year of presence on the WWW, the HGBASE project has compiled data for over 22 000 records, and this number continues to triple every 6–12 months with data harvested or submitted from all major public genome databases and published literature from the previous decade. Extensive annotation enhancement, internal consistency checking and manual review of every record is undertaken to address potential errors and deficiencies sometimes present in the original source data. The fully polished and comprehensive database is made freely available to all at http://hgbase.cgr.ki.se PMID:10592273

Brookes, Anthony J.; Lehvaslaiho, Heikki; Siegfried, Marianne; Boehm, Jana G.; Yuan, Yan P.; Sarkar, Chandra M.; Bork, Peer; Ortigao, Flavio

2000-01-01

334

Tomato Expression Database (TED): a suite of data presentation and analysis tools  

PubMed Central

The Tomato Expression Database (TED) includes three integrated components. The Tomato Microarray Data Warehouse serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. In addition to expression data, TED stores experimental design and array information in compliance with the MIAME guidelines and provides web interfaces for researchers to retrieve data for their own analysis and use. The Tomato Microarray Expression Database contains normalized and processed microarray data for ten time points with nine pair-wise comparisons during fruit development and ripening in a normal tomato variety and nearly isogenic single gene mutants impacting fruit development and ripening. Finally, the Tomato Digital Expression Database contains raw and normalized digital expression (EST abundance) data derived from analysis of the complete public tomato EST collection containing >150?000 ESTs derived from 27 different non-normalized EST libraries. This last component also includes tools for the comparison of tomato and Arabidopsis digital expression data. A set of query interfaces and analysis, and visualization tools have been developed and incorporated into TED, which aid users in identifying and deciphering biologically important information from our datasets. TED can be accessed at . PMID:16381976

Fei, Zhangjun; Tang, Xuemei; Alba, Rob; Giovannoni, James

2006-01-01

335

Women in Politics: Bibliographic Database  

NSDL National Science Digital Library

This bibliographic database currently holds 650 titles of recent works concerned with women in politics. A new addition to the Inter-Parliamentary Union's "Democracy through Partnership between Men and Women in Politics" site, "it provides bibliographic references to books, reports and journal articles on all aspects of women's participation in political life worldwide." The search mechanism allows users to specify type of document, geographic region, publishing organization, subject matter, author, title of periodical, and year of publication. Alternatively, there is also a subject keyword search. For more information about the Inter-Parliamentary Union Website, see the December 12, 1997 Scout Report.

336

International Regulation Database  

NSDL National Science Digital Library

Created and maintained by the Organisation for Economic Co-operation and Development (OECD), the International Regulation Database is a "comprehensive internationally-comparable set of information about the state of regulation and market structures in OECD countries." The contents of the database are derived primarily from an ad hoc questionnaire that was given to OECD member countries in 1998. The database contains over 1,100 variables for each country and includes both broad regulations dealing with product markets, such as "state control of business enterprises" and international trade and investment barriers, as well as sector-specific regulations for areas such as telecommunications, retail distribution, and electricity supply. The database must be downloaded to users's computers, and is offered in both Access and Excel versions. An eleven-page, detailed description of the database's contents, structure, and use is also available, as is a Users' Guide, which offers step-by-step instructions for manipulating the Access database.

337

Acute Toxicity Database  

NSDL National Science Digital Library

This searchable database (by species or chemical) from the US Geological Survey was initially developed in 1986 using some 4,900 acute toxicity tests (since 1969) with 410 chemicals and 66 species of aquatic animals. Two databases may be viewed online (or downloaded): the ID Database (CSV format), including Chemical ID, Chemical Name, Units of Measure, Use of Chemical, and CAS number, and Acute Toxicity Test Results Database, a CSV file with acute toxicity data by Chemical ID. Also available onsite is the "Manual of Acute Toxicity: Interpretation and DataBase for 410 Chemicals and 66 Species of Freshwater Animals." The manual describes the database structure and contents, data quality, and metadata reference information.

338

Reviewing population studies for forensic purposes: Dog mitochondrial DNA  

PubMed Central

Abstract The identification of dog hair through mtDNA analysis has become increasingly important in the last 15 years, as it can provide associative evidence connecting victims and suspects. The evidential value of an mtDNA match between dog hair and its potential donor is determined by the random match probability of the haplotype. This probability is based on the haplotype’s population frequency estimate. Consequently, implementing a population study representative of the population relevant to the forensic case is vital to the correct evaluation of the evidence. This paper reviews numerous published dog mtDNA studies and shows that many of these studies vary widely in sampling strategies and data quality. Therefore, several features influencing the representativeness of a population sample are discussed. Moreover, recommendations are provided on how to set up a dog mtDNA population study and how to decide whether or not to include published data. This review emphasizes the need for improved dog mtDNA population data for forensic purposes, including targeting the entire mitochondrial genome. In particular, the creation of a publicly available database of qualitative dog mtDNA population studies would improve the genetic analysis of dog traces in forensic casework. PMID:24453568

Verscheure, Sophie; Backeljau, Thierry; Desmyter, Stijn

2013-01-01

339

POW/MIA Database  

NSDL National Science Digital Library

POW/MIA Database. Library of Congress, Washington, D.C.: This database assists researchers investigating the U.S. government documents pertaining to U.S. military personnel killed, missing, or imprisoned in Southeast Asia during or after the American involvement in the Vietnam Conflict. The database is searchable by last name, country name, service branch, or keywords, and copies of desired documents may be obtained from the Library of Congress.

340

2010 Worldwide Gasification Database  

DOE Data Explorer

The 2010 Worldwide Gasification Database describes the current world gasification industry and identifies near-term planned capacity additions. The database lists gasification projects and includes information (e.g., plant location, number and type of gasifiers, syngas capacity, feedstock, and products). The database reveals that the worldwide gasification capacity has continued to grow for the past several decades and is now at 70,817 megawatts thermal (MWth) of syngas output at 144 operating plants with a total of 412 gasifiers.

341

Trends in Database Research  

Microsoft Academic Search

Research in databases has played a vital role in developing information system technology and also the outcome of this research\\u000a has been very successful resulting in great potential for industry. The database industry is generating billions of dollars\\u000a of business annually. It has estimated that the database industry itself has generated $42 billion revenue in 2000 and this\\u000a market is

Mukesh K. Mohania; Yahiko Kambayashi; A. Min Tjoa; Roland Wagner; Ladjel Bellatreche

2001-01-01

342

USCM Mayoral Elections Database  

NSDL National Science Digital Library

The US Conference of Mayors (USCM) (see the January 1, 1999 Scout Report) provides the Mayoral Elections Database. The database allows citizens from all 50 states and the District of Columbia to locate information on mayoral elections held in 1999. Users may search the database by city, state, political party, or name of candidate. Searches yield city name, state, party and name of election winner, percentage of votes earned by winner, and month of election. [AO

343

IPSec Database Query Acceleration  

NASA Astrophysics Data System (ADS)

IPSec is a suite of protocols that adds security to communications at the IP level. Protocols within IPSec make extensive use of two databases, namely the Security Policy Database (SPD) and the Security Association Database (SAD). The ability to query the SPD quickly is fundamental as this operation needs to be done for each incoming or outgoing IP packet, even if no IPSec processing needs to be applied on it. This may easily result in millions of query per second in gigabit networks.

Ferrante, Alberto; Chandra, Satish; Piuri, Vincenzo

344

Exploring DNA  

NSDL National Science Digital Library

Get ready to learn an explore DNA, genes and proteins. By moving through the different topics, you will hopefully gain greater understanding of how DNA, genes, and proteins are all related. DNA to Protein Module You will zoom into the human body to see and read more about DNA. The Journey Into DNA DNA Workshop Activity- You try it! More DNA and Protein Synthesis ...

Flitton, Mrs.

2008-08-13

345

The Martian Climate Database  

NSDL National Science Digital Library

This site features access to a database of statistics that was developed in order to describe the climate and surface environment of Mars. The database provides a valuable resource for scientific studies of the Martian atmosphere. The database is based directly on output from multi-annual integrations of two General Circulation Models (GCMs) which were developed jointly at Laboratoire de Météorologie Dynamique du CNRS, Paris, and the University of Oxford, with support from the European Space Agency. The site also includes an online version of a poster that gives examples of database output, including comparisons with previous observations.

Lewis, S. R.; Collins, M.; Read, P. L.; Forget, F.; Fournier, R.; Hourdin, C.

346

THE LATIN MUSIC DATABASE  

E-print Network

In this paper we present the Latin Music Database, a novel database of Latin musical recordings which has been developed for automatic music genre classification, but can also be used in other music information retrieval tasks. The method for assigning genres to the musical recordings is based on human expert perception and therefore capture their tacit knowledge in the genre labeling process. We also present the ethnomusicology of the genres available in the database as it might provide important information for the analysis of the results of any experiment that employs the database. 1

Carlos N. Silla; Alessandro L. Koerich; Celso A. A. Kaestner

347

Backing up DMF Databases  

NASA Technical Reports Server (NTRS)

A complete backup of the Cray Data Migration Facility (DMF) databases should include the data migration databases, all media specific process' (MSP's) databases, and the journal file. The backup should be able to accomplished without impacting users or stopping DMF. The High Speed Processors group at the Numerical Aerodynamics Simulation (NAS) Facility at NASA Ames Research Center undertook the task of finding an effective and efficient way to backup all DMF databases. This has been accomplished by taking advantage of new features introduced in DMF 2.0 and adding a minor modification to the dmdaemon. This paper discusses the investigation and the changes necessary to implement these enhancements.

Cardo, Nicholas P.; Woodrow, Thomas (Technical Monitor)

1994-01-01

348

TCM Database@Taiwan: the world's largest traditional Chinese medicine database for drug screening in silico.  

PubMed

Rapid advancing computational technologies have greatly speeded up the development of computer-aided drug design (CADD). Recently, pharmaceutical companies have increasingly shifted their attentions toward traditional Chinese medicine (TCM) for novel lead compounds. Despite the growing number of studies on TCM, there is no free 3D small molecular structure database of TCM available for virtual screening or molecular simulation. To address this shortcoming, we have constructed TCM Database@Taiwan (http://tcm.cmu.edu.tw/) based on information collected from Chinese medical texts and scientific publications. TCM Database@Taiwan is currently the world's largest non-commercial TCM database. This web-based database contains more than 20,000 pure compounds isolated from 453 TCM ingredients. Both cdx (2D) and Tripos mol2 (3D) formats of each pure compound in the database are available for download and virtual screening. The TCM database includes both simple and advanced web-based query options that can specify search clauses, such as molecular properties, substructures, TCM ingredients, and TCM classification, based on intended drug actions. The TCM database can be easily accessed by all researchers conducting CADD. Over the last eight years, numerous volunteers have devoted their time to analyze TCM ingredients from Chinese medical texts as well as to construct structure files for each isolated compound. We believe that TCM Database@Taiwan will be a milestone on the path towards modernizing traditional Chinese medicine. PMID:21253603

Chen, Calvin Yu-Chian

2011-01-01

349

HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment.  

PubMed

Deep sequencing technologies are completely revolutionizing the approach to DNA analysis. Mitochondrial DNA (mtDNA) studies entered in the "postgenomic era": the burst in sequenced samples observed in nuclear genomics is expected also in mitochondria, a trend that can already be detected checking complete mtDNA sequences database submission rate. Tools for the analysis of these data are available, but they fail in throughput or in easiness of use. We present here a new pipeline based on previous algorithms, inherited from the "nuclear genomic toolbox," combined with a newly developed algorithm capable of efficiently and easily classify new mtDNA sequences according to PhyloTree nomenclature. Detected mutations are also annotated using data collected from publicly available databases. Thanks to the analysis of all freely available sequences with known haplogroup obtained from GenBank, we were able to produce a PhyloTree-based weighted tree, taking into account each haplogroup pattern conservation. The combination of a highly efficient aligner, coupled with our algorithm and massive usage of asynchronous parallel processing, allowed us to build a high-throughput pipeline for the analysis of mtDNA sequences that can be quickly updated to follow the ever-changing nomenclature. HaploFind is freely accessible at the following Web address: https://haplofind.unibo.it. PMID:23696374

Vianello, Dario; Sevini, Federica; Castellani, Gastone; Lomartire, Laura; Capri, Miriam; Franceschi, Claudio

2013-09-01

350

The HITRAN 2008 Molecular Spectroscopic Database  

NASA Technical Reports Server (NTRS)

This paper describes the status of the 2008 edition of the HITRAN molecular spectroscopic database. The new edition is the first official public release since the 2004 edition, although a number of crucial updates had been made available online since 2004. The HITRAN compilation consists of several components that serve as input for radiative-transfer calculation codes: individual line parameters for the microwave through visible spectra of molecules in the gas phase; absorption cross-sections for molecules having dense spectral features, i.e., spectra in which the individual lines are not resolved; individual line parameters and absorption cross sections for bands in the ultra-violet; refractive indices of aerosols, tables and files of general properties associated with the database; and database management software. The line-by-line portion of the database contains spectroscopic parameters for forty-two molecules including many of their isotopologues.

Rothman, Laurence S.; Gordon, Iouli E.; Barbe, Alain; Benner, D. Chris; Bernath, Peter F.; Birk, Manfred; Boudon, V.; Brown, Linda R.; Campargue, Alain; Champion, J.-P.; Chance, Kelly V.; Coudert, L. H.; Sung, K.; Toth, R. A.

2009-01-01

351

Federal Register document image database  

NASA Astrophysics Data System (ADS)

A new, fully-automated process has been developed at NIST to derive ground truth for document images. The method involves matching optical character recognition (OCR) results from a page with typesetting files for an entire book. Public domain software used to derive the ground truth is provided in the form of Perl scripts and C source code, and includes new, more efficient string alignment technology and a word- level scoring package. With this ground truthing technology, it is now feasible to produce much larger data sets, at much lower cost, than was ever possible with previous labor- intensive, manual data collection projects. Using this method, NIST has produced a new document image database for evaluating Document Analysis and Recognition technologies and Information Retrieval systems. The database produced contains scanned images, SGML-tagged ground truth text, commercial OCR results, and image quality assessment results for pages published in the 1994 Federal Register. These data files are useful in a wide variety of experiments and research. There were roughly 250 issues, comprised of nearly 69,000 pages, published in the Federal Register in 1994. This volume of the database contains the pages of 20 books published in January of that year. In all, there are 4711 page images provided, with 4519 of them having corresponding ground truth. This volume is distributed on two ISO-9660 CD- ROMs. Future volumes may be released, depending on the level of interest.

Garris, Michael D.; Janet, Stanley A.; Klein, William W.

1999-01-01

352

Online vs. Print Publications: Users' Opinions.  

ERIC Educational Resources Information Center

The rapid expansion of online publications has raised some concerns about the use of online databases in comparison with using traditional print publications. To determine the opinions of end users about using Dialog online databases versus their corresponding print versions, three libraries in Atlanta, Georgia--Atlanta-Fulton Public Library,…

Wang, Chih

353

Nanotechnology with DNA DNA Nanodevices  

E-print Network

Nanotechnology with DNA DNA Nanodevices Friedrich C. Simmel* and Wendy U. Dittmer A DNA actuator. Introduction.............285 2. Overview: DNA Nanotechnology.......285 3. Prototypes of Nanomechanical DNA overview of DNA nanotechnology as a whole is given. The most important properties of DNA molecules

Ludwig-Maximilians-Universität, München

354

Dictionary as Database.  

ERIC Educational Resources Information Center

Discussion of dictionaries as databases focuses on the digitizing of The Oxford English dictionary (OED) and the use of Standard Generalized Mark-Up Language (SGML). Topics include the creation of a consortium to digitize the OED, document structure, relational databases, text forms, sequence, and discourse. (LRW)

Painter, Derrick

1996-01-01

355

Pharmacoepidemiology and Healthcare Databases  

Cancer.gov

These databases can be used to access national and international data that can help answer some of the outstanding questions of cancer-related outcomes (positive or negative) associated with pharmaceuticals. Some of the databases are linked to a table of pharmacoepidemiology data elements, which provides a snapshot of the material contained therein.

356

Database Reviews: Legal Information.  

ERIC Educational Resources Information Center

Detailed reviews of two legal information databases--"Laborlaw I" and "Legal Resource Index"--are presented in this paper. Each database review begins with a bibliographic entry listing the title; producer; vendor; cost per hour contact time; offline print cost per citation; time period covered; frequency of updates; and size of file. A detailed…

Seiser, Virginia

357

Summarisation for Mobile Databases  

Microsoft Academic Search

In mobile computing, issues such as limited resources, network capacities and organisational constraints may cause the complete replication of large databases on a mobile device to be infeasible. At the same time, some on-board storage of data is attractive as communication to the main database can be inconsistent. Thus, as the emphasis on application mobility increases, data summarisation offers a

Darin Chan; John F. Roddick

2005-01-01

358

A Quality System Database  

NASA Technical Reports Server (NTRS)

A quality system database (QSD), and software to administer the database, were developed to support recording of administrative nonconformance activities that involve requirements for documentation of corrective and/or preventive actions, which can include ISO 9000 internal quality audits and customer complaints.

Snell, William H.; Turner, Anne M.; Gifford, Luther; Stites, William

2010-01-01

359

Biological Macromolecule Crystallization Database  

National Institute of Standards and Technology Data Gateway

SRD 21 Biological Macromolecule Crystallization Database (Web, free access)   The Biological Macromolecule Crystallization Database and NASA Archive for Protein Crystal Growth Data (BMCD) contains the conditions reported for the crystallization of proteins and nucleic acids used in X-ray structure determinations and archives the results of microgravity macromolecule crystallization studies.

360

Criticality safety database  

SciTech Connect

The Nuclear Criticality Safety (NCS) Database is being developed by OSTI at the request of NE-74 to help workers in the area of nuclear criticality safety to accomplish their mission. It is a bibliographic database resident on the OSTI VAX cluster, and can be searched by BASIS software.

Beasley, M.; Rutkowski, R.

1994-09-01

361

Database in Artificial Intelligence.  

ERIC Educational Resources Information Center

Describes a specialist bibliographic database of literature in the field of artificial intelligence created by the Turing Institute (Glasgow, Scotland) using the BRS/Search information retrieval software. The subscription method for end-users--i.e., annual fee entitles user to unlimited access to database, document provision, and printed awareness…

Wilkinson, Julia

1986-01-01

362

HIV Structural Database  

National Institute of Standards and Technology Data Gateway

SRD 102 HIV Structural Database (Web, free access)   The HIV Protease Structural Database is an archive of experimentally determined 3-D structures of Human Immunodeficiency Virus 1 (HIV-1), Human Immunodeficiency Virus 2 (HIV-2) and Simian Immunodeficiency Virus (SIV) Proteases and their complexes with inhibitors or products of substrate cleavage.

363

MUGEN mouse database; animal models of human immunological diseases  

Microsoft Academic Search

The MUGEN mouse database (MMdb) (www.mugen-noe.org\\/database\\/) is a database of murine models of immune processes and immunological diseases. Its aim is to share and publicize information on mouse strain characteristics and availability from participating institutions. MMdb's basic classification of models is based on three major research application categories: Models of Human Disease, Models of Immune Processes and Transgenic Tools. Data

V. Aidinis; C. Chandras; M. Manoloukos; A. Thanassopoulou; K. Kranidioti; M. Armaka; E. Douni; D. L. Kontoyiannis; M. Zouberakis; G. Kollias

2008-01-01

364

Cascadia Tsunami Deposit Database  

USGS Publications Warehouse

The Cascadia Tsunami Deposit Database contains data on the location and sedimentological properties of tsunami deposits found along the Cascadia margin. Data have been compiled from 52 studies, documenting 59 sites from northern California to Vancouver Island, British Columbia that contain known or potential tsunami deposits. Bibliographical references are provided for all sites included in the database. Cascadia tsunami deposits are usually seen as anomalous sand layers in coastal marsh or lake sediments. The studies cited in the database use numerous criteria based on sedimentary characteristics to distinguish tsunami deposits from sand layers deposited by other processes, such as river flooding and storm surges. Several studies cited in the database contain evidence for more than one tsunami at a site. Data categories include age, thickness, layering, grainsize, and other sedimentological characteristics of Cascadia tsunami deposits. The database documents the variability observed in tsunami deposits found along the Cascadia margin.

Peters, Robert; Jaffe, Bruce; Gelfenbaum, Guy; Peterson, Curt

2003-01-01

365

Temporal Database Entries for the Springer Encyclopedia of Database Systems  

E-print Network

Temporal Database Entries for the Springer Encyclopedia of Database Systems Christian S. Jensen Database Entries for the Springer Encyclopedia of Database Systems Copyright c 2009 Springer. All rights. #12;Preface In January 2007 Ling Liu and Tamer ¨Ozsu started work on an Encyclopedia of Database

Snodgrass, Richard T.

366

FORMIDABEL: The Belgian Ants Database  

PubMed Central

Abstract FORMIDABEL is a database of Belgian Ants containing more than 27.000 occurrence records. These records originate from collections, field sampling and literature. The database gives information on 76 native and 9 introduced ant species found in Belgium. The collection records originated mainly from the ants collection in Royal Belgian Institute of Natural Sciences (RBINS), the ‘Gaspar’ Ants collection in Gembloux and the zoological collection of the University of Liège (ULG). The oldest occurrences date back from May 1866, the most recent refer to August 2012. FORMIDABEL is a work in progress and the database is updated twice a year. The latest version of the dataset is publicly and freely accessible through this url: http://ipt.biodiversity.be/resource.do?r=formidabel. The dataset is also retrievable via the GBIF data portal through this link: http://data.gbif.org/datasets/resource/14697 A dedicated geo-portal, developed by the Belgian Biodiversity Platform is accessible at: http://www.formicidae-atlas.be Purpose: FORMIDABEL is a joint cooperation of the Flemish ants working group “Polyergus” (http://formicidae.be) and the Wallonian ants working group “FourmisWalBru” (http://fourmiswalbru.be). The original database was created in 2002 in the context of the preliminary red data book of Flemish Ants (Dekoninck et al. 2003). Later, in 2005, data from the Southern part of Belgium; Wallonia and Brussels were added. In 2012 this dataset was again updated for the creation of the first Belgian Ants Atlas (Figure 1) (Dekoninck et al. 2012). The main purpose of this atlas was to generate maps for all outdoor-living ant species in Belgium using an overlay of the standard Belgian ecoregions. By using this overlay for most species, we can discern a clear and often restricted distribution pattern in Belgium, mainly based on vegetation and soil types. PMID:23794918

Brosens, Dimitri; Vankerkhoven, François; Ignace, David; Wegnez, Philippe; Noé, Nicolas; Heughebaert, André; Bortels, Jeannine; Dekoninck, Wouter

2013-01-01

367

Central Asia Active Fault Database  

NASA Astrophysics Data System (ADS)

The ongoing collision of the Indian subcontinent with Asia controls active tectonics and seismicity in Central Asia. This motion is accommodated by faults that have historically caused devastating earthquakes and continue to pose serious threats to the population at risk. Despite international and regional efforts to assess seismic hazards in Central Asia, little attention has been given to development of a comprehensive database for active faults in the region. To address this issue and to better understand the distribution and level of seismic hazard in Central Asia, we are developing a publically available database for active faults of Central Asia (including but not limited to Afghanistan, Tajikistan, Kyrgyzstan, northern Pakistan and western China) using ArcGIS. The database is designed to allow users to store, map and query important fault parameters such as fault location, displacement history, rate of movement, and other data relevant to seismic hazard studies including fault trench locations, geochronology constraints, and seismic studies. Data sources integrated into the database include previously published maps and scientific investigations as well as strain rate measurements and historic and recent seismicity. In addition, high resolution Quickbird, Spot, and Aster imagery are used for selected features to locate and measure offset of landforms associated with Quaternary faulting. These features are individually digitized and linked to attribute tables that provide a description for each feature. Preliminary observations include inconsistent and sometimes inaccurate information for faults documented in different studies. For example, the Darvaz-Karakul fault which roughly defines the western margin of the Pamir, has been mapped with differences in location of up to 12 kilometers. The sense of motion for this fault ranges from unknown to thrust and strike-slip in three different studies despite documented left-lateral displacements of Holocene and late Pleistocene landforms observed near the fault trace.

Mohadjer, Solmaz; Ehlers, Todd A.; Kakar, Najibullah

2014-05-01

368

Comprehensive thematic T-matrix reference database: A 2013-2014 update  

NASA Astrophysics Data System (ADS)

This paper is the sixth update to the comprehensive thematic database of peer-reviewed T-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2013. It also lists several earlier publications not incorporated in the original database and previous updates.

Mishchenko, Michael I.; Zakharova, Nadezhda T.; Khlebtsov, Nikolai G.; Wriedt, Thomas; Videen, Gorden

2014-10-01

369

Nucleotide sequence databases: a gold mine for biologists  

Microsoft Academic Search

The rapid expansion of nucleotide sequence data available in public databases is revolutionizing biomedical research. These databases have a variety of uses, including the discovery of novel genes, identification of homologous genes, analysis of alternative splicing, chromosomal localization of genes, and detection of polymorphisms. Data sets such as the human transcript map will undoubtedly accelerate identification of candidate genes in

Akhilesh Pandey; Fran Lewitter

1999-01-01

370

Use of a geophysical database in navy operational systems  

Microsoft Academic Search

The Naval Oceanographic Office has constructed a high-resolution geophysical database (GDB) for the Western Barents Sea describing the properties of the seafloor and subsurface sediment layers important to acoustic modeling. The original implementation of this database used a public domain geographic information system (GIS) called GRASS (Geographic Resource Analysis Support System). Subsequent versions use a commercial GIS, ARC\\/INFO. While GRASS

M. Schexnayder; P. Haeger; L. Cadima; E. Holmes

1995-01-01

371

The Vocational Guidance Research Database: A Scientometric Approach  

ERIC Educational Resources Information Center

The scientometric study of scientific output through publications in specialized journals cannot be undertaken exclusively with the databases available today. For this reason, the objective of this article is to introduce the "Base de Datos de Investigacion en Orientacion Vocacional" [Vocational Guidance Research Database], based on the use of…

Flores-Buils, Raquel; Gil-Beltran, Jose Manuel; Caballer-Miedes, Antonio; Martinez-Martinez, Miguel Angel

2012-01-01

372

A catalog of new eclipsing binaries in the Kepler database  

E-print Network

In this thesis, we present a catalog of binary stars discovered in the publicly available Kepler database, none of which were included in previous such catalogs published by the Kepler science team. A brief review of other ...

Kotson, Michael Christopher

2012-01-01

373

THE THERMODYNAMICS OF DNA STRUCTURAL MOTIFS  

Microsoft Academic Search

? Abstract DNA secondary structure plays an important role in biology, geno- typing diagnostics, a variety of molecular biology techniques, in vitro-selected DNA catalysts, nanotechnology, and DNA-based computing. Accurate prediction of DNA secondary structure and hybridization using dynamic programming algorithms requires a database of thermodynamic parameters for several motifs including Watson-Crick base pairs, internal mismatches, terminal mismatches, terminal dangling ends,

John SantaLucia; Donald Hicks

2004-01-01

374

Pfam: the protein families database  

PubMed Central

Pfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and the USA (http://pfam.janelia.org/), is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0. Since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtKB) at nearly 80%, despite a 50% increase in the size of the underlying sequence database. Since our 2012 article describing Pfam, we have also undertaken a comprehensive review of the features that are provided by Pfam over and above the basic family data. For each feature, we determined the relevance, computational burden, usage statistics and the functionality of the feature in a website context. As a consequence of this review, we have removed some features, enhanced others and developed new ones to meet the changing demands of computational biology. Here, we describe the changes to Pfam content. Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures. PMID:24288371

Finn, Robert D.; Bateman, Alex; Clements, Jody; Coggill, Penelope; Eberhardt, Ruth Y.; Eddy, Sean R.; Heger, Andreas; Hetherington, Kirstie; Holm, Liisa; Mistry, Jaina; Sonnhammer, Erik L. L.; Tate, John; Punta, Marco

2014-01-01

375

Novel circular DNA viruses identified in Procordulia grayi and Xanthocnemis zealandica larvae using metagenomic approaches.  

PubMed

Recent advances in sequencing and metagenomics have enabled the discovery of many novel single stranded DNA (ssDNA) viruses from various environments. We have previously demonstrated that adult dragonflies, as predatory insects, are useful indicators of ssDNA viruses in terrestrial ecosystems. Here we recover and characterise 13 viral genomes which represent 10 novel and diverse circular replication associated protein (Rep)-encoding single stranded (CRESS) DNA viruses (1628-2668nt) from Procordulia grayi and Xanthocnemis zealandica dragonfly larvae collected from four high-country lakes in the South Island of New Zealand. The dragonfly larvae associated CRESS DNA viruses have different genome architectures, however, they all encode two major open reading frames (ORFs) which either have bidirectional or unidirectional arrangement. The 13 viral genomes have a conserved NAGTATTAC nonanucleotide motif and in their predicted Rep proteins we identified the rolling circle replication (RCR) motif 1, 2 and 3, as well as superfamily 3 (SF3) helicase motifs. Maximum likelihood phylogenetic and pairwise identity analysis of the Rep amino acid sequences reveal that the dragonfly larvae novel CRESS DNA viruses share <63% pairwise amino acid identity to the Reps of other CRESS DNA viruses whose complete genomes have been determined and available in public databases and that these viruses are novel. CRESS DNA viruses are circulating in larval dragonfly populations; however, we are unable to ascertain whether these viruses are infecting the larvae directly or are transient within dragonflies via their diet. PMID:24462907

Dayaram, Anisha; Galatowitsch, Mark; Harding, Jon S; Argüello-Astorga, Gerardo R; Varsani, Arvind

2014-03-01

376

NIST Standard Reference Database 17 NIST Chemical Kinetics Database  

E-print Network

NIST Standard Reference Database 17 __________________________________________________________ NIST Chemical Kinetics Database WindowsTM Version 2Q98 Users' Guide (NIST) uses its best efforts to deliver a high quality copy of the Database and to verify that the data

377

The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database  

PubMed Central

Databases are an essential tool and resource within the field of bioinformatics. The primary aim of this study was to generate an overview of global bacterial biodiversity and biogeography using available data from the two largest public online databases, NCBI Nucleotide and GBIF. The secondary aim was to highlight the contribution each geographic area has to each database. The basis for data analysis of this study was the metadata provided by both databases, mainly, the taxonomy and the geographical area origin of isolation of the microorganism (record). These were directly obtained from GBIF through the online interface, while E-utilities and Python were used in combination with a programmatic web service access to obtain data from the NCBI Nucleotide Database. Results indicate that the American continent, and more specifically the USA, is the top contributor, while Africa and Antarctica are less well represented. This highlights the imbalance of exploration within these areas rather than any reduction in biodiversity. This study describes a novel approach to generating global scale patterns of bacterial biodiversity and biogeography and indicates that the Proteobacteria are the most abundant and widely distributed phylum within both databases. PMID:24228241

James, Phillip; Nateche, Farida; Wellington, Elizabeth M. H.; Hacene, Hocine

2013-01-01

378

The Gaia Parameter Database  

NASA Astrophysics Data System (ADS)

The parallel development of many aspects of a complex mission like Gaia, which includes numerous participants in ESA, industrial companies, and a large and active scientific collaboration throughout Europe, makes keeping track of the many design changes, instrument and operational complexities, and numerical values for the data analysis a very challenging problem. A comprehensive, easily-accessible, up-to-date, and definitive compilation of a large range of numerical quantities is required, and the Gaia parameter database has been established to satisfy these needs. The database is a centralised repository containing, besides mathematical, physical, and astronomical constants, many satellite and subsystem design parameters. At the end of 2004, more than 1600 parameters had been included. Version control has been implemented, providing, next to a `live' version with the most recent parameters, well-defined reference versions of the full database contents. The database can be queried or browsed using a regular Web browser (http://www.rssd.esa.int/Gaia/paramdb). Query results are formated by default in HTML. Data can also be retrieved as Fortran-77, Fortran-90, Java, ANSIC, C++, or XML structures for direct inclusion into software codes in these languages. The idea is that all collaborating scientists can use the database parameters and values, once retrieved, directly linked to computational routines. An off-line access mode is also available, enabling users to automatically download the contents of the database. The database will be maintained actively, and significant extensions of the contents are planned. Consistent use in the future of the database by the Gaia community at large, including all industrial teams, will ensure correct numerical values throughout the complex software systems being built up as details of the Gaia design develop. The database is already being used for the telemetry simulation chain in ESTEC, and in the data simulations for GDAAS2.

de Bruijne, J. H. J.; Lammers, U.; Perryman, M. A. C.

2005-01-01

379

SyStemCell: A Database Populated with Multiple Levels of Experimental Data from Stem Cell Differentiation Research  

PubMed Central

Elucidation of the mechanisms of stem cell differentiation is of great scientific interest. Increasing evidence suggests that stem cell differentiation involves changes at multiple levels of biological regulation, which together orchestrate the complex differentiation process; many related studies have been performed to investigate the various levels of regulation. The resulting valuable data, however, remain scattered. Most of the current stem cell-relevant databases focus on a single level of regulation (mRNA expression) from limited stem cell types; thus, a unifying resource would be of great value to compile the multiple levels of research data available. Here we present a database for this purpose, SyStemCell, deposited with multi-level experimental data from stem cell research. The database currently covers seven levels of stem cell differentiation-associated regulatory mechanisms, including DNA CpG 5-hydroxymethylcytosine/methylation, histone modification, transcript products, microRNA-based regulation, protein products, phosphorylation proteins and transcription factor regulation, all of which have been curated from 285 peer-reviewed publications selected from PubMed. The database contains 43,434 genes, recorded as 942,221 gene entries, for four organisms (Homo sapiens, Mus musculus, Rattus norvegicus, and Macaca mulatta) and various stem cell sources (e.g., embryonic stem cells, neural stem cells and induced pluripotent stem cells). Data in SyStemCell can be queried by Entrez gene ID, symbol, alias, or browsed by specific stem cell type at each level of genetic regulation. An online analysis tool is integrated to assist researchers to mine potential relationships among different regulations, and the potential usage of the database is demonstrated by three case studies. SyStemCell is the first database to bridge multi-level experimental information of stem cell studies, which can become an important reference resource for stem cell researchers. The database is available at http://lifecenter.sgst.cn/SyStemCell/. PMID:22807998

Zeng, Lingyao; Sun, Jiehuan; Li, Wei; Sun, Han; He, Ying; Li, Jing; Zhang, Guoqing; Wang, Chuan; Li, Yixue; Xie, Lu

2012-01-01

380

SyStemCell: a database populated with multiple levels of experimental data from stem cell differentiation research.  

PubMed

Elucidation of the mechanisms of stem cell differentiation is of great scientific interest. Increasing evidence suggests that stem cell differentiation involves changes at multiple levels of biological regulation, which together orchestrate the complex differentiation process; many related studies have been performed to investigate the various levels of regulation. The resulting valuable data, however, remain scattered. Most of the current stem cell-relevant databases focus on a single level of regulation (mRNA expression) from limited stem cell types; thus, a unifying resource would be of great value to compile the multiple levels of research data available. Here we present a database for this purpose, SyStemCell, deposited with multi-level experimental data from stem cell research. The database currently covers seven levels of stem cell differentiation-associated regulatory mechanisms, including DNA CpG 5-hydroxymethylcytosine/methylation, histone modification, transcript products, microRNA-based regulation, protein products, phosphorylation proteins and transcription factor regulation, all of which have been curated from 285 peer-reviewed publications selected from PubMed. The database contains 43,434 genes, recorded as 942,221 gene entries, for four organisms (Homo sapiens, Mus musculus, Rattus norvegicus, and Macaca mulatta) and various stem cell sources (e.g., embryonic stem cells, neural stem cells and induced pluripotent stem cells). Data in SyStemCell can be queried by Entrez gene ID, symbol, alias, or browsed by specific stem cell type at each level of genetic regulation. An online analysis tool is integrated to assist researchers to mine potential relationships among different regulations, and the potential usage of the database is demonstrated by three case studies. SyStemCell is the first database to bridge multi-level experimental information of stem cell studies, which can become an important reference resource for stem cell researchers. The database is available at http://lifecenter.sgst.cn/SyStemCell/. PMID:22807998

Yu, Jian; Xing, Xiaobin; Zeng, Lingyao; Sun, Jiehuan; Li, Wei; Sun, Han; He, Ying; Li, Jing; Zhang, Guoqing; Wang, Chuan; Li, Yixue; Xie, Lu

2012-01-01

381

CMD: a Cotton Microsatellite Database resource for Gossypium genomics  

Microsoft Academic Search

BACKGROUND: The Cotton Microsatellite Database (CMD) http:\\/\\/www.cottonssr.org is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding. DESCRIPTION: At present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays

Anna Blenda; Jodi Scheffler; Brian Scheffler; Michael Palmer; Jean-Marc Lacape; John Z Yu; Christopher Jesudurai; Sook Jung; Sriram Muthukumar; Preetham Yellambalase; Stephen Ficklin; Margaret Staton; Robert Eshelman; Mauricio Ulloa; Sukumar Saha; Ben Burr; Shaolin Liu; Tianzhen Zhang; Deqiu Fang; Alan Pepper; Siva Kumpatla; John Jacobs; Jeff Tomkins; Roy Cantrell; Dorrie Main

2006-01-01

382

World Cave Database  

NSDL National Science Digital Library

The World Cave Database was created by Eric Madelaine of the French Research Institute for Computer Science and Automatic Control. Users can browse the database by depth, length, or an alphabetical listing of the caves, and can search the nearly 1000 entries by keyword. All included caves are 300 meters deep and 3 kilometers long and larger, including the longest, which is the Mammoth Cave system in the US that is known to be 563,270 meters long. After getting used to the somewhat cryptic layout of cave listings, users should find the database a useful and informative resource.

383

World Biodiversity Database  

NSDL National Science Digital Library

The World Biodiversity Database, provided by the Expert Center for Taxonomic Identification (ETI), seeks to "document all presently known species (about 1.7 million) and to make this important biological information worldwide accessible." This continually growing database "provides taxonomic information, species names, synonyms, descriptions, illustrations and literature references when available" on 200,000 taxa. The searchable database can be explored using an expandable tree of the five taxonomic kingdoms or by typing in a common or scientific name. Both educators and students should find this site easy to navigate, informative, and useful.

384

The Press Freedom Database  

NSDL National Science Digital Library

Developed by the Committee to Protect Journalists (CPJ), The Press Freedom Database contains case histories of documented press freedom violations against journalists and media organizations worldwide as well as annual CPJ reports on the violations in specific countries and regions. The case histories document the circumstances in which journalists have been attacked, killed, expelled, censored, harassed, threatened, and/or imprisoned. The database is searchable by journalist name, news organization, type of organization, date, country, or region. Currently, the database, which is updated weekly, contains over 2,000 reports of press freedom violations, spanning from 1993 to the present.

385

World Biodiversity Database  

NSDL National Science Digital Library

The World Biodiversity Database, provided by ETI BioInformatics, seeks to document all presently known species (about 1.7 million) and to make this important biological information worldwide accessible. This continually growing database provides "taxonomic information, species names, synonyms, descriptions, illustrations and literature references, as well as online identification keys and interactive geographical information systems." The searchable database can be explored using an expandable tree of taxonomic kingdoms or by typing in a common or scientific name. Both educators and students should find this site easy to navigate, informative, and useful.

2005-12-08

386

Year 2000 Reports Database  

NSDL National Science Digital Library

The US Securities and Exchange Commission (SEC) has recently released this searchable database of Y2K readiness reports in order to disclose the preparatory efforts of the securities industry. The database contains more than 13,000 reports from the broker-dealers, transfer agents, investment advisors, and mutual funds required to file with the SEC. Reports include descriptions of the company's, agent's, or fund's state of Y2K readiness, costs to address the Y2K problem, Y2K risks, and contingency plans. Complete database documentation, search instructions, and contact information are provided at the Important Information page.

1999-01-01

387

Household Products Database  

NSDL National Science Digital Library

Users will find important and possibly life-saving information on over 4,000 household products in this online database from the National Library of Medicine's Specialized Information Services. The database allows users to find out what a product contains, potential health effects, and safety and handling information. Users can quickly and easily search the database by product name, ingredients, or symptom. The products search seems to be the most user-friendly, as it is organized alphabetically and by general category, e.g. home maintenance, personal care/use, auto products, and so on.

388

Phase Equilibria Diagrams Database  

National Institute of Standards and Technology Data Gateway

SRD 31 NIST/ACerS Phase Equilibria Diagrams Database (PC database for purchase)   The Phase Equilibria Diagrams Database contains commentaries and more than 21,000 diagrams for non-organic systems, including those published in all 21 hard-copy volumes produced as part of the ACerS-NIST Phase Equilibria Diagrams Program (formerly titled Phase Diagrams for Ceramists): Volumes I through XIV (blue books); Annuals 91, 92, 93; High Tc Superconductors I & II; Zirconium & Zirconia Systems; and Electronic Ceramics I. Materials covered include oxides as well as non-oxide systems such as chalcogenides and pnictides, phosphates, salt systems, and mixed systems of these classes.

389

The Mendel Database  

NSDL National Science Digital Library

The Mendel Database, part of the Mendel Plant Gene Nomenclature Database project by the Mendel Bioinformatics Group (UK), "aims to develop a common nomenclature for sequenced genes, based on gene families, for all photosynthetic organisms, the organelle genomes of both photosynthetic and non-photosynthetic organisms (fungi, algae, and protozoa) and plant viruses." At present, the searchable database contains "more than 20,000 genes, which can be translated into proteins, organized into about 2,000 gene families based on their sequence homology." Typical entries include gene family number and gene family name, "Gene & Gene Product descriptions & synonyms, and Accession numbers with links to SWISS-PROT & EMBL."

390

Databases for materials selection  

SciTech Connect

The Cambridge Materials Selector (CMS2.0) materials database was developed by the Engineering Dept. at Cambridge University in the United Kingdom. This database makes it possible to select a material for a specific application from essentially all classes of materials. Genera, Predict, and Socrates software programs from CLI International, Houston, Texas, automate materials selection and corrosion problem-solving tasks. They are said to significantly reduce the time necessary to select a suitable material and/or to assess a corrosion problem and reach cost-effective solutions. This article describes both databases and tells how to use them.

NONE

1996-06-01

391

The Hanford NCTSP database  

SciTech Connect

A topical, knowledge-screened, comprehensive database of the nuclear criticality safety literature was assembled in the late 1980s and expanded on through 1995. The activity was sponsored by the US Department of Energy Nuclear Criticality Technical Safety Project (NCTSP). The database covers 50 yr of criticality safety documentation and contains more than 3100 references. In 1998, the database was moved to the Nuclear Criticality Safety Program Lawrence Livermore National Laboratory (LLNL) Web site and can be accessed by criticality safety practitioners at http://ncsc.llnl.gov.

Toffer, H.; Erickson, D.G.

2000-07-01

392

DNA microarray (spot) .  

E-print Network

1. DNA microarray DNA (spot) . DNA probe , probe (hybridization) . DNA microarray cDNA oligonucleotide oligonucleotide cDNA probe . oligonucleotide microarray , DNA , probe . oligonucleotide microarray probe

393

Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.  

PubMed

A contig-oriented database for annotation of the rice genome has been constructed to facilitate map-based rice genomics. The Rice Annotation Database has the following functional features: (i) extensive effort of manual annotations of P1-derived artificial chromosome/bacterial artificial chromosome clones can be merged at chromosome and contig-level; (ii) concise visualization of the annotation information such as the predicted genes, results of various prediction programs (RiceHMM, Genscan, Genscan+, Fgenesh, GeneMark, etc.), homology to expressed sequence tag, full-length cDNA and protein; (iii) user-friendly clone / gene query system; (iv) download functions for nucleotide, amino acid and coding sequences; (v) analysis of various features of the genome (GC-content, average value, etc.); and (vi) genome-wide homology search (BLAST) of contig- and chromosome-level genome sequence to allow comparative analysis with the genome sequence of other organisms. As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results including 30 000 manually curated genes. The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome. The database can be accessed at http://rad.dna.affrc.go.jp/. PMID:15608281

Ito, Yuichi; Arikawa, Kohji; Antonio, Baltazar A; Ohta, Isamu; Naito, Shinji; Mukai, Yoshiyuki; Shimano, Atsuko; Masukawa, Masatoshi; Shibata, Michie; Yamamoto, Mayu; Ito, Yukiyo; Yokoyama, Junri; Sakai, Yasumichi; Sakata, Katsumi; Nagamura, Yoshiaki; Namiki, Nobukazu; Matsumoto, Takashi; Higo, Kenichi; Sasaki, Takuji

2005-01-01

394

Toward unification of taxonomy databases in a distributed computer environment  

SciTech Connect

All the taxonomy databases constructed with the DNA databases of the international DNA data banks are powerful electronic dictionaries which aid in biological research by computer. The taxonomy databases are, however not consistently unified with a relational format. If we can achieve consistent unification of the taxonomy databases, it will be useful in comparing many research results, and investigating future research directions from existent research results. In particular, it will be useful in comparing relationships between phylogenetic trees inferred from molecular data and those constructed from morphological data. The goal of the present study is to unify the existent taxonomy databases and eliminate inconsistencies (errors) that are present in them. Inconsistencies occur particularly in the restructuring of the existent taxonomy databases, since classification rules for constructing the taxonomy have rapidly changed with biological advancements. A repair system is needed to remove inconsistencies in each data bank and mismatches among data banks. This paper describes a new methodology for removing both inconsistencies and mismatches from the databases on a distributed computer environment. The methodology is implemented in a relational database management system, SYBASE.

Kitakami, Hajime [Hiroshima City Univ. (Japan); Tateno, Yoshio; Gojobori, Takashi [National Institute of Genetics, Shizuoka-Ken (Japan)

1994-12-31

395

A web-database of mammalian morphology and a reanalysis of placental phylogeny  

PubMed Central

Background Recent publications concerning the interordinal phylogeny of placental mammals have converged on a common signal, consisting of four major radiations with some ambiguity regarding the placental root. The DNA data with which these relationships have been reconstructed are easily accessible from public databases; access to morphological characters is much more difficult. Here, I present a graphical web-database of morphological characters focusing on placental mammals, in tandem with a combined-data phylogenetic analysis of placental mammal phylogeny. Results The results reinforce the growing consensus regarding the extant placental mammal clades of Afrotheria, Xenarthra, Euarchontoglires, and Laurasiatheria. Unweighted parsimony applied to all DNA sequences and insertion-deletion (indel) characters of extant taxa alone support a placental root at murid rodents; combined with morphology this shifts to Afrotheria. Bayesian analyses of morphology, indels, and DNA support both a basal position for Afrotheria and the position of Cretaceous eutherians outside of crown Placentalia. Depending on treatment of third codon positions, the affinity of several fossils (Leptictis,Paleoparadoxia, Plesiorycteropus and Zalambdalestes) vary, highlighting the potential effect of sequence data on fossils for which such data are missing. Conclusion The combined dataset supports the location of the placental mammal root at Afrotheria or Xenarthra, not at Erinaceus or rodents. Even a small morphological dataset can have a marked influence on the location of the root in a combined-data analysis. Additional morphological data are desirable to better reconstruct the position of several fossil taxa; and the graphic-rich, web-based morphology data matrix presented here will make it easier to incorporate more taxa into a larger data matrix. PMID:17608930

Asher, Robert J

2007-01-01

396

Complex Carbohydrate Research Center Spectral Databases  

NSDL National Science Digital Library

Dr. William York of the Complex Carbohydrate Research Center has created these two databases with scientific input from others at the University of Georgia. The Xyloglucan NMR Database consists of a searchable table of the ?H-NMR chemical shifts of xyloglucan oligoglycosyl alditols. Xyloglucans are highly branched polymers with a cellulosic backbone (i.e., consisting of b-(1,4)-linked D-glucosyl residues). The basis for the most commonly used nomenclature for xyloglucan structures comes from the linear array of glycosyl side chains that many of the backbone residues bear. The Partially Methylated Alditol Acetate (PMAA) Database shows the molecular structures of PMAAs derived from Hexopyranosyl, Pentopyranosyl, and Pentofuranosyl Residues. Users view the structures by gliding the mouse over a table. The PMAA Database also says that electron-impact mass spectra are available, but at the time of publication, these links weren't working. The Xyloglucan database comes with overviews, search guides, and nomenclature information. The PMAA database has a help page. Both require a free login.

York, William ..

2001-01-01

397

Database of Mechanical Properties of Textile Composites  

NASA Technical Reports Server (NTRS)

This report describes the approach followed to develop a database for mechanical properties of textile composites. The data in this database is assembled from NASA Advanced Composites Technology (ACT) programs and from data in the public domain. This database meets the data documentation requirements of MIL-HDBK-17, Section 8.1.2, which describes in detail the type and amount of information needed to completely document composite material properties. The database focuses on mechanical properties of textile composite. Properties are available for a range of parameters such as direction, fiber architecture, materials, environmental condition, and failure mode. The composite materials in the database contain innovative textile architectures such as the braided, woven, and knitted materials evaluated under the NASA ACT programs. In summary, the database contains results for approximately 3500 coupon level tests, for ten different fiber/resin combinations, and seven different textile architectures. It also includes a limited amount of prepreg tape composites data from ACT programs where side-by-side comparisons were made.

Delbrey, Jerry

1996-01-01

398

Proposal for a High Energy Nuclear Database  

E-print Network

We propose to develop a high-energy heavy-ion experimental database and make it accessible to the scientific community through an on-line interface. This database will be searchable and cross-indexed with relevant publications, including published detector descriptions. Since this database will be a community resource, it requires the high-energy nuclear physics community's financial and manpower support. This database should eventually contain all published data from Bevalac, AGS and SPS to RHIC and LHC energies, proton-proton to nucleus-nucleus collisions as well as other relevant systems, and all measured observables. Such a database would have tremendous scientific payoff as it makes systematic studies easier and allows simpler benchmarking of theoretical models to a broad range of old and new experiments. Furthermore, there is a growing need for compilations of high-energy nuclear data for applications including stockpile stewardship, technology development for inertial confinement fusion and target and source development for upcoming facilities such as the Next Linear Collider. To enhance the utility of this database, we propose periodically performing evaluations of the data and summarizing the results in topical reviews.

David A. Brown Ramona Vogt

2005-04-01

399

Corruption of genomic databases with anomalous sequence.  

PubMed Central

We describe evidence that DNA sequences from vectors used for cloning and sequencing have been incorporated accidentally into eukaryotic entries in the GenBank database. These incorporations were not restricted to one type of vector or to a single mechanism. Many minor instances may have been the result of simple editing errors, but some entries contained large blocks of vector sequence that had been incorporated by contamination or other accidents during cloning. Some cases involved unusual rearrangements and areas of vector distant from the normal insertion sites. Matches to vector were found in 0.23% of 20,000 sequences analyzed in GenBank Release 63. Although the possibility of anomalous sequence incorporation has been recognized since the inception of GenBank and should be easy to avoid, recent evidence suggests that this problem is increasing more quickly than the database itself. The presence of anomalous sequence may have serious consequences for the interpretation and use of database entries, and will have an impact on issues of database management. The incorporated vector fragments described here may also be useful for a crude estimate of the fidelity of sequence information in the database. In alignments with well-defined ends, the matching sequences showed 96.8% identity to vector; when poorer matches with arbitrary limits were included, the aggregate identity to vector sequence was 94.8%. PMID:1614861

Lamperti, E D; Kittelberger, J M; Smith, T F; Villa-Komaroff, L

1992-01-01

400

Effort Gap Database  

NSDL National Science Digital Library

Maintained by the Biological Resources Research Center (BRRC) at the University of Nevada, Reno, the Effort Gap Database organizes information on biological research efforts in the Great Basin. Users may search the database (by multiple topics) for current and past projects, or they may add new information to the database. Typical returns provide information such as project title, scientific goals, available data, Principal Investigators, temporal and spatial scale of research, habitats in study area, types of organisms, source of funding, and finished products. Designed as an interactive Web application to allow and encourage researchers to share research foci and learn about other conservation biology projects in Nevada, this database is an excellent example of how to facilitate collaboration across multiple ecological scales and agencies.

401

CAL Learning Strategies Database  

NSDL National Science Digital Library

The Learning Strategies Database, developed by the Center for Advancement of Learning (CAL) at Muskingum College, organizes information about learning strategies into four major sections: Introduction to the CAL Learning Strategies Database, General-Purpose Learning Strategies, Content-Specific Learning Strategies, and Bibliography of Learning Strategies Resources. Each section is further divided into more specific subsections, creating a hierarchical database structure. For example, the general-purpose section contains sixteen subsections related to general learning, such as Memory, Test Preparation, and Notetaking; whereas, the content-specific section has 27 disciplinary subsections, covering subjects in the natural sciences, social sciences, humanities, and arts. The information in the database allows students of all ages and their instructors to assess current learning styles, and to identify and implement methods for effective education adapted to the learning strengths and weaknesses of individual students.

402

Bishop Museum: Ichthyology Databases  

NSDL National Science Digital Library

This website offers access to three on-line fish database sites from the Bishop Museum in Hawaii. The first database, the Bishop Museum Hawaiian Fish Checklist, contains 980 records and offers search fields for Genus, Order, Species, Family, and more. The second site, the Fuji Fish Searchable Database, is under construction but is still operational and includes search criteria for Taxa (with our without specimens), Taxon, and Locality. The third database, the Bishop Museum Zooarchaeology Laboratory Fish Osteology Collection, "is searchable by order, family, genus, species, common and local names, locality and status (whether endemic, indigenous, or non-indigenous). Bishop Museum's comparative reference collection is available for use by students and researchers interested in identifying fish remains from archaeological sites in Hawaii and elsewhere in the Pacific."

403

The Biotech Database  

NSDL National Science Digital Library

This prototype database was developed to allow regulatory officials in the OECD (Organisation for Economic Co-operation and Development) to share information about biotechnologically derived products that have been approved for commercialization or are in the process of being approved. The contents of the database have been provided on a voluntary basis from OECD member countries and institutions developing biotech products. Users can view the database contents by organism or developing country, search by keyword, or construct customized biotech products tables. As the site notes, this database is not intended to be a comprehensive listing of all biotech products, but rather an aid to information-sharing. A number of related links are offered at the bottom of the homepage.

404

Database lists endangered languages  

E-print Network

of slang originally used by British fairground communities, but later adopted by gay subcultures as a type of code. See more about: Software Features database endangered languages world oral literature project Loading... /div> View...

Woollacott, Emma

2010-12-10

405

Native Health Research Database  

MedlinePLUS

... THIS APP WITH JAVASCRIPT TURNED OFF. THE NATIVE HEALTH DATABASE REQUIRES JAVASCRIPT IN ORDER TO FUNCTION. PLEASE ... Data and Links, U.S. Census Bureau American Indian Health from the National Library of Medicine Arctic Health ...

406

The International Nucleotide Sequence Database Collaboration.  

PubMed

The members of the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org) set out to capture, preserve and present globally comprehensive public domain nucleotide sequence information. The work of the long-standing collaboration includes the provision of data formats, annotation conventions and routine global data exchange. Among the many developments to INSDC resources in 2011 are the newly launched BioProject database and improved handling of assembly information. In this article, we outline INSDC services and update the reader on developments in 2011. PMID:22080546

Karsch-Mizrachi, Ilene; Nakamura, Yasukazu; Cochrane, Guy

2012-01-01

407

SAbDab: the structural antibody database.  

PubMed

Structural antibody database (SAbDab; http://opig.stats.ox.ac.uk/webapps/sabdab) is an online resource containing all the publicly available antibody structures annotated and presented in a consistent fashion. The data are annotated with several properties including experimental information, gene details, correct heavy and light chain pairings, antigen details and, where available, antibody-antigen binding affinity. The user can select structures, according to these attributes as well as structural properties such as complementarity determining region loop conformation and variable domain orientation. Individual structures, datasets and the complete database can be downloaded. PMID:24214988

Dunbar, James; Krawczyk, Konrad; Leem, Jinwoo; Baker, Terry; Fuchs, Angelika; Georges, Guy; Shi, Jiye; Deane, Charlotte M

2014-01-01

408

SSME environment database development  

NASA Technical Reports Server (NTRS)

The internal environment of the Space Shuttle Main Engine (SSME) is being determined from hot firings of the prototype engines and from model tests using either air or water as the test fluid. The objectives are to develop a database system to facilitate management and analysis of test measurements and results, to enter available data into the the database, and to analyze available data to establish conventions and procedures to provide consistency in data normalization and configuration geometry references.

Reardon, John

1987-01-01

409

Automated Pattern Database Design  

Microsoft Academic Search

Pattern databases are dictionaries for heuristic estimates based on state-to-goal distances in state space abstractions. Their effectiveness is sensitive to the selection of the under- lying patterns. Especially for multiple and additive pattern databases, a manual selection of pattern sets that lead to good exploration results is involved. For automating the selection process, greedy bin-packing strategies have been suggested. This

Stefan Edelkamp

410

Chemical Synthesis Database  

NSDL National Science Digital Library

This database provides information on thousands of chemical compounds, including synthesis references and physical properties. The database is searchable by keyword and browseable by journal title. For each compound, the information includes molecular formula and weight, Chemical Abstracts Service (CAS) numbers, International Chemical Identifier (InChIKey), and Simplified Molecular Input Line Entry System (SMILES) notation. There is also information on synonyms, physical properties (boiling and melting points, density), an illustration of chemical structure, spectral data, and links to additional data.

411

Ecomp Executive Compensation Database  

NSDL National Science Digital Library

The Ecomp Executive Compensation Database allows users to research the compensation and net-worth of executives. Users may search the database by company name or ticker symbol, as well as by state, sector, and industry pull-down menus. Search returns list compensation summaries for the top executives, including salary, bonus, and total compensation. Clicking on the executive's name will give a more detailed summary, including restricted stock, LTIP payouts, and value realized for options exercised. All numbers are for 1999.

412

ECOTOX Database System  

NSDL National Science Digital Library

The US Environmental Protection Agency (EPA) provides this database of chemical toxicity. Three individual EPA databases are combined to provide information on chemical-specific toxicity values for aquatic and terrestrial plants and animals. Users can search for research reports by chemical name, species name, or environmental effect. The site has informative help files and browse features. This Web site is useful for evaluating industrial chemicals or for environmental assessment research.

2000-01-01

413

Statistical Database Security  

Microsoft Academic Search

Statistical database security focuses on the protection of confidential individual values stored in so-called statistical databases and used for statistical purposes. Examples include patient records used by medical researchers, and detailed phone call\\u000a records, statistically analyzed by phone companies in order to improve their services. This problem became apparent in the\\u000a 1970s and has escalated in recent years due to

Ljiljana Brankovic; Helen Giggins

414

ICE Biological Inventories Databases  

NSDL National Science Digital Library

The Information Center for the Environment (ICE) is a cooperative effort between scientists at University of California -- Davis and collaborators from over thirty organizations involved in environmental protection." The ICE Biological Inventory Databases contain "documented, taxonomically standardized species inventories of plants and animals reported from the world's protected areas." New to the Scout Report, these online databases have been updated recently to include botanical inventories from protected areas in Costa Rica and South Africa.

2000-01-01

415

Virus Information Database  

NSDL National Science Digital Library

Symantec Corporation's AntiVirus Research Center has recently released a virus information database that includes over 10,000 computer viruses. The searchable and browseable database can include information about aliases for each virus, infection length, area of infection, likelihood of infection, region reported, characteristics, target platform and target date, in addition to a brief description of how the virus works. The site also provides a basic tutorial on viruses. Symantec, under the Norton name, produces several anti-virus products.

416

Querying genomic databases  

SciTech Connect

A natural-language interface has been developed that retrieves genomic information by using a simple subset of English. The interface spares the biologist from the task of learning database-specific query languages and computer programming. Currently, the interface deals with the E. coli genome. It can, however, be readily extended and shows promise as a means of easy access to other sequenced genomic databases as well.

Baehr, A.; Hagstrom, R.; Joerg, D.; Overbeek, R.

1991-09-01

417

TCC Trade Agreements Database  

NSDL National Science Digital Library

Developed by the Department of Commerce to aid US exporters, the Trade Compliance Center (TCC) provides access to more than 200 trade documents via the Trade Related Agreements Database (TARA). US Trade Agreements may be browsed by country signatory, issue, or agreement title, or searched by keyword with the benefit on an online thesaurus. In addition, the TCC provides a related database of Market Access Information with searchable country commercial guides, reports on economic policy and trade practices, and national trade estimate reports.

1998-01-01

418

NASA scientific and technical publications: A catalog of special publications, reference publications, conference publications, and technical papers, 1987-1990  

NASA Technical Reports Server (NTRS)

This catalog lists 783 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into NASA Scientific and Technical Information Database during the year's 1987 through 1990. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

1991-01-01

419

NASA scientific and technical publications: A catalog of Special Publications, Reference Publications, Conference Publications, and Technical Papers, 1987  

NASA Technical Reports Server (NTRS)

This catalog lists 239 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered in the NASA scientific and technical information database during accession year 1987. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

1988-01-01

420

NASA scientific and technical publications: A catalog of special publications, reference publications, conference publications, and technical papers, 1991-1992  

NASA Technical Reports Server (NTRS)

This catalog lists 458 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into the NASA Scientific and Technical Information database during accession year 1991 through 1992. The entries are grouped by subject category. Indexes of subject terms, personal authors, and NASA report numbers are provided.

1993-01-01

421

Crude Oil Analysis Database  

DOE Data Explorer

The composition and physical properties of crude oil vary widely from one reservoir to another within an oil field, as well as from one field or region to another. Although all oils consist of hydrocarbons and their derivatives, the proportions of various types of compounds differ greatly. This makes some oils more suitable than others for specific refining processes and uses. To take advantage of this diversity, one needs access to information in a large database of crude oil analyses. The Crude Oil Analysis Database (COADB) currently satisfies this need by offering 9,056 crude oil analyses. Of these, 8,500 are United States domestic oils. The database contains results of analysis of the general properties and chemical composition, as well as the field, formation, and geographic location of the crude oil sample. [Taken from the Introduction to COAMDATA_DESC.pdf, part of the zipped software and database file at http://www.netl.doe.gov/technologies/oil-gas/Software/database.html] Save the zipped file to your PC. When opened, it will contain PDF documents and a large Excel spreadsheet. It will also contain the database in Microsoft Access 2002.

Shay, Johanna Y.

422

Clinician use of a pediatric cardiology database on a microcomputer.  

PubMed

A pediatric cardiology database was designed and implemented on a microcomputer using the MEDUS/A (Harvard School of Public Health) database management system. This database has potential utility in the areas of clinical research, patient management, and administration. Initial uses of the system include a study of ventricular septal defects, and automation of pacemaker clinic and cardiac catheterization laboratory records. Clinicians with little or no programming experience can alter the database structure and tailor complicated applications to their particular needs. Preliminary evaluation of the system is presented. PMID:3841043

Soffer, L J; Wolfenson, L B; Sivakoff, M C

1985-12-01

423

PARALLEL DATABASE MACHINES Kjell Bratbergsengen  

E-print Network

PARALLEL DATABASE MACHINES Kjell Bratbergsengen Department of Computer Systems and Telematics in the Database Technology Group at The Department of Computer Systems and Telematics, NTH has been supported

424

Cleaving DNA with DNA  

NASA Astrophysics Data System (ADS)

A DNA structure is described that can cleave single-stranded DNA oligonucleotides in the presence of ionic copper. This ``deoxyribozyme'' can self-cleave or can operate as a bimolecular complex that simultaneously makes use of duplex and triplex interactions to bind and cleave separate DNA substrates. Bimolecular deoxyribozyme-mediated strand scission proceeds with a kobs of 0.2 min-1, whereas the corresponding uncatalyzed reaction could not be detected. The duplex and triplex recognition domains can be altered, making possible the targeted cleavage of single-stranded DNAs with different nucleotide sequences. Several small synthetic DNAs were made to function as simple ``restriction enzymes'' for the site-specific cleavage of single-stranded DNA.

Carmi, Nir; Balkhi, Shameelah R.; Breaker, Ronald R.

1998-03-01

425

PlantGDB, plant genome database and analysis tools  

Microsoft Academic Search

PlantGDB (http:\\/\\/www.plantgdb.org\\/) is a database of molecular sequence data for all plant species with significant sequencing efforts. The database organizes EST sequences into contigs that repre- sent tentative unique genes. Contigs are annotated and, whenever possible, linked to their respective genomic DNA. Genome sequence fragments are assembled similarly. The goal of the PlantGDB web site is to establish the basis

Qunfeng Dong; Shannon D. Schlueter; Volker Brendel

2004-01-01

426

Illinois State Archives: Database of Illinois Civil War Veterans  

NSDL National Science Digital Library

This database from the Illinois State Archives "indexes the first eight volumes of the nine volume publication, Report of the Adjutant General of the State of Illinois." The publication is drawn from the original rosters maintained during the Civil War by the Adjutant General. In addition to the names of approximately 250,000 men organized into 175 regiments, this searchable database also provides histories of the Illinois units and regiments. The database was created and donated to the Illinois State Archives by amateur genealogist Fred Delap of Kansas, Illinois.

427

Databases and Software for NMR-Based Metabolomics  

PubMed Central

New software and increasingly sophisticated NMR metabolite spectral databases are advancing the unique abilities of NMR spectroscopy to identify and quantify small molecules in solution for studies of metabolite biomarkers and metabolic flux. Public and commercial databases now contain experimental 1D 1H, 13C and 2D 1H-13C spectra and extracted spectral parameters for over a thousand compounds and theoretical data for thousands more. Public databases containing experimental NMR data from complex metabolic studies are emerging. These databases are providing information vital for the construction and testing of new computational algorithms for NMR-based chemometric and quantitative metabolomics studies. In this review we focus on database and software tools that support a quantitative NMR approach to the analysis of 1D and 2D NMR spectra of complex biological mixtures. PMID:24260723

Ellinger, James J.; Chylla, Roger A.; Ulrich, Eldon L.; Markley, John L.

2013-01-01

428

Space medicine research publications: 1983-1984  

NASA Technical Reports Server (NTRS)

A list of publications supported by the Space Medicine Program, Office of Space Science and Applications is given. Included are publications entered into the Life Sciences Bibliographic Database by The George Washington University as of October 1, 1984.

Solberg, J. L.; Pleasant, L. G.

1984-01-01

429

The GLIMS Glacier Database: a spatio-temporal database  

E-print Network

The GLIMS Glacier Database: a spatio-temporal database implemented using Open Source tools Bruce countries #12;#12;#12;#12;#12;System components PostgreSQL (relational database) PostGIS (geospatial) GDAL (Geospatial Data Abstraction Library) Perl, PHP, Shapelib, ... #12;GLIMS Glacier Database System

Raup, Bruce H.

430

A Database Interface for Clustering in Large Spatial Databases  

Microsoft Academic Search

Both the number and the size of spatial databases are rapidly growing because of the large amount of data obtained from satellite images, X-ray crystallography or other scientific equipment. Therefore, automated knowledge discovery be- comes more and more important in spatial databases. So far, most of the methods for knowledge discovery in databases (KDD) have been based on relational database

Martin Ester; Hans-peter Kriegel; Xiaowei Xu

1995-01-01

431

AtlasT4SS: A curated database for type IV secretion systems  

PubMed Central

Background The type IV secretion system (T4SS) can be classified as a large family of macromolecule transporter systems, divided into three recognized sub-families, according to the well-known functions. The major sub-family is the conjugation system, which allows transfer of genetic material, such as a nucleoprotein, via cell contact among bacteria. Also, the conjugation system can transfer genetic material from bacteria to eukaryotic cells; such is the case with the T-DNA transfer of Agrobacterium tumefaciens to host plant cells. The system of effector protein transport constitutes the second sub-family, and the third one corresponds to the DNA uptake/release system. Genome analyses have revealed numerous T4SS in Bacteria and Archaea. The purpose of this work was to organize, classify, and integrate the T4SS data into a single database, called AtlasT4SS - the first public database devoted exclusively to this prokaryotic secretion system. Description The AtlasT4SS is a manual curated database that describes a large number of proteins related to the type IV secretion system reported so far in Gram-negative and Gram-positive bacteria, as well as in Archaea. The database was created using the RDBMS MySQL and the Catalyst Framework based in the Perl programming language and using the Model-View-Controller (MVC) design pattern for Web. The current version holds a comprehensive collection of 1,617 T4SS proteins from 58 Bacteria (49 Gram-negative and 9 Gram-Positive), one Archaea and 11 plasmids. By applying the bi-directional best hit (BBH) relationship in pairwise genome comparison, it was possible to obtain a core set of 134 clusters of orthologous genes encoding T4SS proteins. Conclusions In our database we present one way of classifying orthologous groups of T4SSs in a hierarchical classification scheme with three levels. The first level comprises four classes that are based on the organization of genetic determinants, shared homologies, and evolutionary relationships: (i) F-T4SS, (ii) P-T4SS, (iii) I-T4SS, and (iv) GI-T4SS. The second level designates a specific well-known protein families otherwise an uncharacterized protein family. Finally, in the third level, each protein of an ortholog cluster is classified according to its involvement in a specific cellular process. AtlasT4SS database is open access and is available at http://www.t4ss.lncc.br. PMID:22876890

2012-01-01

432

gender Inn: Women's and Gender Studies Database  

NSDL National Science Digital Library

This searchable bibliographic database contains records describing over 5,000 works on "feminist theory, feminist literary criticism and gender studies focusing on English and American literature" from 1950 to the present. The search form is available under the heading Research, where users may indicate which field to search, limit by year of publication, and specify whether to return results in English or German. Works included in the database have been assigned up to 20 keywords from a locally-developed thesaurus for feminist research. A German version of the thesaurus is available in the Deutsche (German) Version and work is underway to translate the thesaurus into English. Work on this database was started in 1987 by Professor Natasha Wurzbach of the University of Cologne (Germany) English Department, and was made accessible via the Internet through a cooperative project with the Department of Art and Design at the Fachhochschule Koln.

1997-01-01

433

The AGN Black Hole Mass Database  

E-print Network

The AGN Black Hole Mass Database is a compilation of all published spectroscopic reverberation-mapping studies of active galaxies. We have created a public web interface, where users may get the most up-to-date black hole masses from reverberation mapping for any particular active galactic nucleus (AGN), as well as obtain the individual measurements upon which the masses are based and the appropriate references. While the database currently focuses on the measurements necessary for black hole mass determinations, we also plan to expand it in the future to include additional useful information, such as host-galaxy characteristics. New reverberation mapping results will also be incorporated into the database as they are published in peer-refereed journals.

Bentz, Misty C

2014-01-01

434

Sandia Wind Turbine Loads Database  

DOE Data Explorer

The Sandia Wind Turbine Loads Database is divided into six files, each corresponding to approximately 16 years of simulation. The files are text files with data in columnar format. The 424MB zipped file containing six data files can be downloaded by the public. The files simulate 10-minute maximum loads for the NREL 5MW wind turbine. The details of the loads simulations can be found in the paper: “Decades of Wind Turbine Loads Simulations”, M. Barone, J. Paquette, B. Resor, and L. Manuel, AIAA2012-1288 (3.69MB PDF). Note that the site-average wind speed is 10 m/s (class I-B), not the 8.5 m/s reported in the paper.

435

Catalog of databases and reports  

SciTech Connect

This catalog provides information about the many reports and materials made available by the US Department of Energy`s (DOE`s) Global Change Research Program (GCRP) and the Carbon Dioxide Information Analysis Center (CDIAC). The catalog is divided into nine sections plus the author and title indexes: Section A--US Department of Energy Global Change Research Program Research Plans and Summaries; Section B--US Department of Energy Global Change Research Program Technical Reports; Section C--US Department of Energy Atmospheric Radiation Measurement (ARM) Program Reports; Section D--Other US Department of Energy Reports; Section E--CDIAC Reports; Section F--CDIAC Numeric Data and Computer Model Distribution; Section G--Other Databases Distributed by CDIAC; Section H--US Department of Agriculture Reports on Response of Vegetation to Carbon Dioxide; and Section I--Other Publications.

Burtis, M.D. [comp.

1997-04-01

436

ADANS database specification  

SciTech Connect

The purpose of the Air Mobility Command (AMC) Deployment Analysis System (ADANS) Database Specification (DS) is to describe the database organization and storage allocation and to provide the detailed data model of the physical design and information necessary for the construction of the parts of the database (e.g., tables, indexes, rules, defaults). The DS includes entity relationship diagrams, table and field definitions, reports on other database objects, and a description of the ADANS data dictionary. ADANS is the automated system used by Headquarters AMC and the Tanker Airlift Control Center (TACC) for airlift planning and scheduling of peacetime and contingency operations as well as for deliberate planning. ADANS also supports planning and scheduling of Air Refueling Events by the TACC and the unit-level tanker schedulers. ADANS receives input in the form of movement requirements and air refueling requests. It provides a suite of tools for planners to manipulate these requirements/requests against mobility assets and to develop, analyze, and distribute schedules. Analysis tools are provided for assessing the products of the scheduling subsystems, and editing capabilities support the refinement of schedules. A reporting capability provides formatted screen, print, and/or file outputs of various standard reports. An interface subsystem handles message traffic to and from external systems. The database is an integral part of the functionality summarized above.

NONE

1997-01-16

437

Global Invasive Species Database  

NSDL National Science Digital Library

The Global Invasive Species Database was developed by the Invasive Species Specialist Group (ISSG), an international group of 100+ scientific and policy experts with the Species Survival Commission (SSC) of the International Union for the Conservation of Nature (IUCN). The entry page of the Website offers background information on invasive species and instructions on how to use the database. A section entitled 100 of the worst (ranging from Rat to Purple Loosestrife) gives viewers an idea of the type of information that will be included in the database, both in terms of expected detail and organizational structure of the database. Types of information provided for each species include Ecology, Distribution, Habitat Matches, References, and Contacts. In addition, a Predictive feature allows viewers to predict the expansion of invasive species, and the Early Warning System matches habitats that the species has already invaded with "other similar habitats around the world." Although still under construction, this database should be a powerful tool for researchers and educators, once completed.

438

Shuttle Hypervelocity Impact Database  

NASA Technical Reports Server (NTRS)

With three flights remaining on the manifest, the shuttle impact hypervelocity database has over 2800 entries. The data is currently divided into tables for crew module windows, payload bay door radiators and thermal protection system regions, with window impacts compromising just over half the records. In general, the database provides dimensions of hypervelocity impact damage, a component level location (i.e., window number or radiator panel number) and the orbiter mission when the impact occurred. Additional detail on the type of particle that produced the damage site is provided when sampling data and definitive analysis results are available. The paper will provide details and insights on the contents of the database including examples of descriptive statistics using the impact data. A discussion of post flight impact damage inspection and sampling techniques that were employed during the different observation campaigns will be presented. Future work to be discussed will be possible enhancements to the database structure and availability of the data for other researchers. A related database of ISS returned surfaces that are under development will also be introduced.

Hyde, James I.; Christiansen, Eric I.; Lear, Dana M.

2011-01-01

439

Shuttle Hypervelocity Impact Database  

NASA Technical Reports Server (NTRS)

With three missions outstanding, the Shuttle Hypervelocity Impact Database has nearly 3000 entries. The data is divided into tables for crew module windows, payload bay door radiators and thermal protection system regions, with window impacts compromising just over half the records. In general, the database provides dimensions of hypervelocity impact damage, a component level location (i.e., window number or radiator panel number) and the orbiter mission when the impact occurred. Additional detail on the type of particle that produced the damage site is provided when sampling data and definitive analysis results are available. Details and insights on the contents of the database including examples of descriptive statistics will be provided. Post flight impact damage inspection and sampling techniques that were employed during the different observation campaigns will also be discussed. Potential enhancements to the database structure and availability of the data for other researchers will be addressed in the Future Work section. A related database of returned surfaces from the International Space Station will also be introduced.

Hyde, James L.; Christiansen, Eric L.; Lear, Dana M.

2011-01-01

440

Using the Reactome Database  

PubMed Central

There is considerable interest in the bioinformatics community in creating pathway databases. The Reactome project (a collaboration between the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Medical Center and the European Bioinformatics Institute) is one such pathway database and collects structured information on all the biological pathways and processes in the human. It is an expert-authored and peer-reviewed, curated collection of well-documented molecular reactions that span the gamut from simple intermediate metabolism to signaling pathways and complex cellular events. This information is supplemented with likely orthologous molecular reactions in mouse, rat, zebrafish, worm and other model organisms. This unit describes how to use the Reactome database to learn the steps of a biological pathway; navigate and browse through the Reactome database; identify the pathways in which a molecule of interest is involved; use the Pathway and Expression analysis tools to search the database for and visualize possible connections within user-supplied experimental data set and Reactome pathways; and the Species Comparison tool to compare human and model organism pathways. PMID:22700314

Haw, Robin

2012-01-01

441

Optical DNA  

NASA Astrophysics Data System (ADS)

A certificate of authenticity (COA) is an inexpensive physical object with a random and unique structure S which is hard to near-exactly replicate. An inexpensive device should be able to scan object’s physical “fingerprint,” a set of features that represents S. In this paper, we explore one set of requirements that optical media such as DVDs should satisfy, to be considered as COAs. As manufacturing of such media produces inevitable errors, we use the locations and count of these errors as a “fingerprint” for each optical disc: its optical DNA. The “fingerprint” is signed using publisher’s private-key and the resulting signature is stored onto the optical medium using a post-production process. Standard DVD players with altered firmware that includes publisher’s public-key, should be able to verify the authenticity of DVDs protected with optical DNA. Our key finding is that for the proposed protocol, only DVDs with exceptional wear-and-tear characteristics would result in an inexpensive and viable anti-counterfeiting technology.

Vijaywargi, Deepak; Lewis, Dave; Kirovski, Darko

442

48 CFR 504.602-71 - Federal Procurement Data System-Public access to data.  

Code of Federal Regulations, 2010 CFR

...System—Public access to data. (a) The FPDS database . The General Services Administration awarded...operation of the Federal Procurement Data System (FPDS) database. That database includes information reported by departments...

2010-10-01

443

78 FR 49730 - Collection of Information; Proposed Extension of Approval; Comment Request-Publicly Available...  

Federal Register 2010, 2011, 2012, 2013

...Available Consumer Product Safety Information Database AGENCY: Consumer Product Safety Commission...Available Consumer Product Safety Information Database. The Commission will consider all comments...maintain a publicly available, searchable database on the safety of consumer products...

2013-08-15

444

48 CFR 504.602-71 - Federal Procurement Data System-Public access to data.  

Code of Federal Regulations, 2011 CFR

...System—Public access to data. (a) The FPDS database . The General Services Administration awarded...operation of the Federal Procurement Data System (FPDS) database. That database includes information reported by departments...

2011-10-01

445

DNA Computing Hamiltonian path  

E-print Network

2014 DNA DNA #12;DNA Computing · Feynman · Adleman · DNASIMD · ... · · · · · DNADNA #12;DNA · DNA · · · · DNA · · #12;2000 2005 2010 1995 Hamiltonian path DNA tweezers DNA tile DNA origami DNA box Sierpinski DNA tile self assembly DNA logic gates Whiplash PCR DNA automaton DNA spider MAYA

Hagiya, Masami

446

Loading databases using dataflow parallelism  

Microsoft Academic Search

This paper describes a parallel database load prototype for Digital's Rdb database product. The prototype takes a dataflow approach to database parallelism. It includes an explorer that discovers and records the cluster configuration in a database, a client CUI interface that gathers the load job description from the user and from the Rdb catalogs, and an optimizer that picks the

Tom Barclay; Robert Barnes; Jim Gray; Prakash Sundaresan

1994-01-01

447

Database Sampling with Functional Dependencies  

E-print Network

Database Sampling with Functional Dependencies Jes´us Bisbal, Jane Grimson Department of Computer there is a need to prototype the database which the applications will use when in operation. A prototype database can be built by sampling data from an existing database. Including relevant semantic information when

Riera, Jesús Bisbal

448

DNA Restriction  

NSDL National Science Digital Library

The discovery of enzymes that could cut and paste DNA made genetic engineering possible. Restriction enzymes, found naturally in bacteria, can be used to cut DNA fragment at specific sequences, while another enzyme, DNA ligase, can attach or rejoin DNA fragments with complementary ends. This animation from Cold Spring Harbor Laboratory's Dolan DNA Learning Center presents DNA restriction through a series of illustrations of processes involved.

2011-11-25

449

Speechdat-e: five eastern european speech databases for voice-operated teleservices completed  

Microsoft Academic Search

In the Speechdat-E project five medium large telephonespeech databases have been collected for Czech, Hungarian,Polish, Russian, and Slovak. The project was recentlyconcluded. This paper reports briefly on the contents of thedatabases, elaborates on experiences gained from the datarecordings and from the validation of the databases. Theavailability of the databases to the public is addressed, too.

Henk van den Heuvel; Jérôme Boudy; Zsolt Bakcsi; Jan Cernocký; Valery Galunov; Julia Kochanina; Wojciech Majewski; Petr Pollák; Milan Rusko; Jerzy Sadowski; Piotr Staroniewicz; Herbert S. Tropf

2001-01-01

450

The Vera am Mittag German audio-visual emotional speech database  

Microsoft Academic Search

The lack of publicly available annotated databases is one of the major barriers to research advances on emotional informa- tion processing. In this contribution we present a recently col- lected database of spontaneous emotional speech in German which is being made available to the research community. The database consists of 12 hours of audio-visual recordings of the German TV talk

Michael Grimm; Kristian Kroschel; Shrikanth Narayanan

2008-01-01

451

Scottish Emigration Database  

NSDL National Science Digital Library

Scotland has given the world a great many things, and during the 19th century, many Scots set sail to seek their fortune in other parts of the world. Social historians and others will be glad to know that the University of Aberdeen's Centre for Irish and Scottish Studies has created this online database of Scottish emigrants. Currently, visitors can examine the records of over 21,000 passengers who embarked at Glasgow and Greenock for other ports. While the database only covers a small time period, the database is well-designed for general use. First-time visitors should take a look at the "User Guide", which includes details about the different fields used in each record, such as "occupation", "urban district/village", and "destination port".

452

FAOSTAT: FAO Statistical Databases  

NSDL National Science Digital Library

In 1997 the Food and Agriculture Organization (FAO) of the United Nations made available several searchable databases containing extensive agricultural data from many countries. Data is provided for production, trade, commodity supply and demand balances, population, land use, and fisheries. Users can select geographical areas, commodities or products, variables relating to those commodities or products, and an annual time series ranging from as early as 1961, depending on the series. Results can be downloaded as text tables, bar or line graphs with user definable axes, or CSV file format -- text with comma separated values for easy import into spreadsheet or other statistical applications. It is important to carefully read the help files that accompany each database in order to fully exploit the searching system. The FAOSTAT Databases give the user access to an amazing amount of country data.

1997-01-01

453

SODA: Solar Radiation Database  

NSDL National Science Digital Library

The Solar Database, or SoDa, is described as an integration and exploitation of networked Solar radiation Databases for environment monitoring and as a project that aims to integrate European-wide solar radiation resources (i.e. databases, processing chains and educational resources) into one, thematically organized, Web site. The search tool allows users to search for data from a variety of sources including Long Term Time Series Data, Climatological Data, Simulation of Radiation Under Clear Skies Data, Solar Energy Systems Data, and much more. Once a particular set is located, the user can view a description of the source and contents of the data, as well as click on the provided links to access them.

454

The SIMBAD astronomical database  

E-print Network

Simbad is the reference database for identification and bibliography of astronomical objects. It contains identifications, `basic data', bibliography, and selected observational measurements for several million astronomical objects. Simbad is developed and maintained by CDS, Strasbourg. Building the database contents is achieved with the help of several contributing institutes. Scanning the bibliography is the result of the collaboration of CDS with bibliographers in Observatoire de Paris (DASGAL), Institut d'Astrophysique de Paris, and Observatoire de Bordeaux. When selecting catalogues and tables for inclusion, priority is given to optimal multi-wavelength coverage of the database, and to support of research developments linked to large projects. In parallel, the systematic scanning of the bibliography reflects the diversity and general trends of astronomical research. A WWW interface to Simbad is available at: http://simbad.u-strasbg.fr/Simbad

Marc Wenger; Francois Ochsenbein; Daniel Egret; Pascal Dubois; Francois Bonnarel; Suzanne Borde; Francoise Genova; Gerard Jasniewicz; Suzanne Laloe; Soizick Lesteven; Richard Monier

2000-02-04

455

New World Fruits Database  

NSDL National Science Digital Library

Hosted by the International Plant Genetic Resources Institute, this database was developed as an information resource on fruits from the Americas. Based on a September 2004 assessment, the New Worlds Fruits Database contained information about "1253 fruit species belonging to 302 genera and 69 families." Species profiles include vernacular names, geographic distribution, uses, bibliographic references, and links to additional Internet resources. Text searches can be conducted by Genus, Species, and Vernacular Name. Drop-down menus are available for several search fields including Family, Fruit Part, Product, Floristic Region, and Region or Country of Origin. The Fruits Database is still under development, and scientists, fruit growers, and other knowledgeable persons are encouraged to submit information and suggestions.

2010-05-13

456

International Architecture Database  

NSDL National Science Digital Library

Drawing on the contributions from persons across much of Europe, the International Architecture Database website has served as a valuable clearinghouse for thousands of architectural projects (both built and unrealized) since 1996. Currently, the database contains information on more than 13,000 projects, most from the 20th and 21st centuries. Visitors can begin by browsing the database by name, location, or keyword. Looking at a single record, visitors will be presented with a host of information, such as building type, primary architect, location, years of construction, and in certain cases with external links, photographs, and plans. Looking through the lists of keywords can actually be quite useful, as each keyword is linked to examples that are demonstrative of the idea suggested by the keyword, such as early Gothic or elementary school. Overall, this is a fine resource for those persons who wish to learn a bit more about architecture or for those looking for information on different architectural projects.

457

Cities and Buildings Database  

NSDL National Science Digital Library

The University of Washington Libraries Digital Collection online projects and archives are well-regarded, and this database proves to be no exception to that highly positive trend. Started in 1995, the Cities and Buildings Database contains over 10,000 digitized images of buildings and cities culled from all historical periods and from all over the world. Visitors may wish to start with a simple keyword search or if they are interested in merely browsing by country, they may do so as well from the homepage. Of course, one should not be surprised to also learn that visitors may also perform detailed searches for buildings by city, style, title, architect, and date of construction. Just to give prospective visitors some sense of the depth and breadth of the collection, the database contains everything from conceptual sketches of Frank Gehry's Experience Music Project to photographs of the monastery of St. Keghard in Armenia.

458

Six New Paleomagnetic Databases released  

NASA Astrophysics Data System (ADS)

The annual update of the International Association of Geomagnetism and Aeronomy (IAGA)-sponsored paleomagnetic databases has now been completed. The databases are available as files for use with Access 2.0 (for Windows 3.1) or Access 97 (for Windows 95) as described by McElhinny and Lock “ 1996”. The new package (Version 3.3 of the databases) now includes six databases as follows: Global Paleomagnetic Database (gpmdb2. mdb orgpmdb97.mdb); Magnetostratigraphy Database (magst2.mdb or magst97.mdb); Paleointensity Database (pint2.mdb orpint97.mdb); Polarity Transitions Database (trans2.mdb or trans97.mdb); Secular Variations Database (secvr2.mdb or secvr97.mdb); and Paleosecular Variation from Lavas Database (psvrl2.mdb or psvrl97.mdb).

McElhinny, Michael W.

459

DataBase on Demand  

NASA Astrophysics Data System (ADS)

At CERN a number of key database applications are running on user-managed MySQL database services. The database on demand project was born out of an idea to provide the CERN user community with an environment to develop and run database services outside of the actual centralised Oracle based database services. The Database on Demand (DBoD) empowers the user to perform certain actions that had been traditionally done by database administrators, DBA's, providing an enterprise platform for database applications. It also allows the CERN user community to run different database engines, e.g. presently open community version of MySQL and single instance Oracle database server. This article describes a technology approach to face this challenge, a service level agreement, the SLA that the project provides, and an evolution of possible scenarios.

Gaspar Aparicio, R.; Gomez, D.; Coterillo Coz, I.; Wojcik, D.

2012-12-01

460

ENZYME: Enzyme Nomenclature Database  

NSDL National Science Digital Library

Recently updated, the ENZYME: Enzyme Nomenclature Database is based mainly on recommendations by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and "describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided." An online user manual describes how to access and use the database, which may be searched by EC number, enzyme class, official description or alternative name(s), chemical compound, or cofactor. Typical returns include Names, Reaction catalyzed, Comments, Human Genetic Diseases, and a host of hyperlinked cross-references. ENZYME is provided by the Swiss Institute of Bioinformatics.

461

HIV Molecular Immunology Database  

NSDL National Science Digital Library

The HIV Molecular Immunology Database, associated with the Los Alamos National Laboratory, the University of California, and the US Department of Energy, "is an annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites." Links are provided to a number of other tools, as well as the associated HIV Immunology Database Compendia, which is downloadable in Adobe Acrobat (.pdf) format. The search functions are fairly easy to use with several drop down boxes to select the fields of interest.

2008-10-01

462

Chinese Movie Database  

NSDL National Science Digital Library

An English version of the Chinese Movie Database has recently been made available. Edited by Lu Pin, the database covers Chinese movies made in mainland China, Hong Kong, Taiwan, and other countries/regions from 1905 to the present. Users can search by movie title or by individual's name or select movie titles from the Movie Index Page. Search returns for individuals include films they have starred in, directed, or written. Returns for film titles include region, language, and hyperlinked production and acting credits.

1996-01-01

463

Chico State Herbarium Database  

NSDL National Science Digital Library

With over 88,000 mounted and dried specimens, the "Biological Sciences Herbarium at California State University, Chico is the most complete repository of plant specimens from northeastern California. The emphasis is on the local flora, and includes a number of rare, threatened, and endangered plant species." Samples in the Herbarium include ferns, conifers, flowering plants, lichens, bryophytes, and slime molds. The Herbarium Database is still adding specimen label information. The Database includes search fields for Genus, Species, and Subspecies. All higher academic institutions are eligible fo